LIBRARY PREPARATION METHODS AND COMPOSITIONS AND USES THEREFOR

Abstract

 Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.

Description

RELATED APPLICATIONS

[0001] This application claims priority to and the benefit under 35 USC § 119(e) of each of U.S. Provisional Application no. 62/527,893 filed June 30, 2017, U.S. Provisional Application no. 62/614,362, filed January 6, 2018, and U.S. Provisional Application no. 62/685,424, filed June 15, 2018. The entire contents of each of the aforementioned applications are herein incorporated by reference in their entirety.

SEQUENCE LISTING

[0002] This application hereby incorporates by reference the material of the electronic Sequence Listing filed concurrently herewith. The material in the electronic Sequence Listing is submitted as a text (.txt) file entitled "20180627_LT01273_ST25.txt" created on June 27, 2018 which has a file size of 359 KB and is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

[0003] The present invention relates to methods of preparing a library of target nucleic acid sequences and compositions and uses therefor.

BRIEF SUMMARY OF THE INVENTION

[0004] Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.

[0005] One aspect of the invention comprises methods for preparing a library of target nucleic acid sequences. In certain embodiments the methods comprise contacting a nucleic acid sample with a plurality of adaptors wherein each of a pair of adaptors are capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification. The methods further comprise digesting the resulting first amplification products to reduce or eliminate any primer dimers resulting in the reaction and preparing partially digested amplicons, thereby preparing resulting gapped, double stranded partially digested amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired products in a second amplification using universal primers to thereby produce a library of target nucleic acid sequences. Each of the plurality of adaptors used in the provided methods comprise a 5' universal handle sequence and a 3' target nucleic acid sequence and a cleavable moiety. Two or more target specific adaptor pairs are included for use in provided methods, wherein each of the 3' target specific sequences comprise cleavable moieties. Optionally, one or more tag sequences are included.

[0006] In another aspect of the invention methods for preparing a library of target nucleic acid sequences having unique tag sequences is provided. In certain embodiments the methods comprise contacting a nucleic acid sample with a plurality of adaptors wherein each of a pair of adaptors are capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification. The methods further comprise digesting the resulting first amplification products to reduce or eliminate any primer dimers resulting in the reaction and preparing partially digested amplicons, thereby preparing resulting gapped, double stranded partially digested amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired products in a second amplification using universal primers to thereby produce a library of target nucleic acid sequences. Each of the plurality of adaptors used in the provided methods comprise a 5' universal handle sequence, one or more unique tag sequences and a 3' target nucleic acid sequence and a cleavable moiety. Two or more target specific adaptor pairs are included for use in provided methods, wherein each of the 3' target specific sequences comprise cleavable moieties, each tag sequence is flanked by cleavable moieties, and each universal handle is without cleavable moieties.

[0007] In a further aspect, compositions are provided. In some embodiments provided are compositions comprising nucleic acid libraries generated by the methods described herein. In other embodiments, compositions comprising a plurality of nucleic acid adaptors are provided, wherein each of the plurality of adaptors comprise a 5' universal handle sequence, one or more unique tag sequences, and a 3' target nucleic acid sequence wherein each adaptor comprises a cleavable moiety. In certain embodiments the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety. In certain embodiments, compositions include at least two and up to one hundred thousand target specific adaptor pairs.

[0008] Still further, uses of provided compositions and kits comprising provided compositions for analysis of sequences of the nucleic acid libraries are additional aspects of the invention. In some embodiments, analysis of the sequences of the resulting libraries enables detection of low frequency alleles in a sample of interest.

[0009] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

[0010] Efficient methods for production of targeted libraries from complex samples is desirable for a variety of nucleic acid analyses. The present invention provides, inter alia, methods of preparing libraries of target nucleic acid sequences, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences; and resulting library compositions are useful for a variety of applications, including sequencing applications. Novel features of the invention are set forth with particularity in the appended claims; and a complete understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

FIGURE 1 depicts a workflow method of the invention that enables efficient rapid, highly multiplexed library preparation.

FIGURE 2 depicts results from the experimental description in Example 2A.

FIGURE 3 depicts results from the experimental description in Example 2B.

FIGURE 4A-4C depicts results from the experimental description in Example 4.

FIGURE 5 depicts results from the experimental description in Example 5.

FIGURE 6A-6C depicts results from the experimental description in Example 6.

FIGURE 7 depicts an additional aspect of the workflow of the invention that enables addition of adaptor sequences to facilitate bidirectional sequencing

FIGURE 8 depicts an additional aspect of the workflow of the invention that enables sequencing on Illumina platforms

DESCRIPTION OF THE INVENTION

[0011] Section headings used herein are for organizational purposes only and are not to be construed as limiting the described subject matter in any way. All literature and similar materials cited in this application, including but not limited to, patents, patent applications, articles, books, treatises, and internet web pages are expressly incorporated by reference in their entirety for any purpose. When definitions of terms in incorporated references appear to differ from the definitions provided in the present teachings, the definition provided in the present teachings shall control. It will be appreciated that there is an implied "about" prior to the temperatures, concentrations, times, etc discussed in the present teachings, such that slight and insubstantial deviations are within the scope of the present teachings herein. In this application, the use of the singular includes the plural unless specifically stated otherwise. It is noted that, as used in this specification, singular forms "a," "an," and "the," and any singular use of a word, include plural referents unless expressly and unequivocally limited to one referent. Also, the use of "comprise", "comprises", "comprising", "contain", "contains", "containing", "include", "includes", and "including" are not intended to be limiting. It is to be understood that both the general description is exemplary and explanatory only and not restrictive of the invention.

[0012] Unless otherwise defined, scientific and technical terms used in connection with the invention described herein shall have the meanings that are commonly understood by those of ordinary skill in the art. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. Generally, nomenclatures utilized in connection with, and techniques of, cell and tissue culture, molecular biology, and protein and oligo-or polynucleotide chemistry and hybridization used herein are those well-known and commonly used in the art. Standard techniques are used, for example, for nucleic acid purification and preparation, chemical analysis, recombinant nucleic acid, and oligonucleotide synthesis. Enzymatic reactions and purification techniques are performed according to manufacturer's specifications or as commonly accomplished in the art or as described herein. Techniques and procedures described herein are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the instant specification. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (Third ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. 2000). Unless specifically provided, any nomenclature utilized in connection with, and laboratory procedures and techniques described herein are those well-known and commonly used in the art. As utilized in accordance with embodiments provided herein, the following terms, unless otherwise indicated, shall be understood to have the following meanings:

[0013] As used herein, "amplify", "amplifying" or "amplification reaction" and their derivatives, refer generally to an action or process whereby at least a portion of a nucleic acid molecule (referred to as a template nucleic acid molecule) is replicated or copied into at least one additional nucleic acid molecule. The additional nucleic acid molecule optionally includes sequence that is substantially identical or substantially complementary to at least some portion of the template nucleic acid molecule. A template target nucleic acid molecule may be single-stranded or double-stranded. The additional resulting replicated nucleic acid molecule may independently be single-stranded or double-stranded. In some embodiments, amplification includes a template-dependent in vitro enzyme-catalyzed reaction for the production of at least one copy of at least some portion of a target nucleic acid molecule or the production of at least one copy of a target nucleic acid sequence that is complementary to at least some portion of a target nucleic acid molecule. Amplification optionally includes linear or exponential replication of a nucleic acid molecule. In some embodiments, such amplification is performed using isothermal conditions; in other embodiments, such amplification can include thermocycling. In some embodiments, the amplification is a multiplex amplification that includes simultaneous amplification of a plurality of target sequences in a single amplification reaction. At least some target sequences can be situated on the same nucleic acid molecule or on different target nucleic acid molecules included in a single amplification reaction. In some embodiments, "amplification" includes amplification of at least some portion of DNA- and/or RNA-based nucleic acids, whether alone, or in combination. An amplification reaction can include single or double-stranded nucleic acid substrates and can further include any amplification processes known to one of ordinary skill in the art. In some embodiments, an amplification reaction includes polymerase chain reaction (PCR). In some embodiments, an amplification reaction includes isothermal amplification.

[0014] As used herein, "amplification conditions" and derivatives (e.g., conditions for amplification, etc.) generally refers to conditions suitable for amplifying one or more nucleic acid sequences. Amplification can be linear or exponential. In some embodiments, amplification conditions include isothermal conditions or alternatively include thermocyling conditions, or a combination of isothermal and themocycling conditions. In some embodiments, conditions suitable for amplifying one or more target nucleic acid sequences includes polymerase chain reaction (PCR) conditions. Typically, amplification conditions refer to a reaction mixture that is sufficient to amplify nucleic acids such as one or more target sequences, or to amplify an amplified target sequence ligated or attached to one or more adaptors, e.g., an adaptor-attached amplified target sequence. Generally, amplification conditions include a catalyst for amplification or for nucleic acid synthesis, for example a polymerase; a primer that possesses some degree of complementarity to the nucleic acid to be amplified; and nucleotides, such as deoxyribonucleoside triphosphates (dNTPs) to promote extension of a primer once hybridized to a nucleic acid. Amplification conditions can require hybridization or annealing of a primer to a nucleic acid, extension of the primer and a denaturing step in which the extended primer is separated from the nucleic acid sequence undergoing amplification. Typically, though not necessarily, amplification conditions can include thermocycling. In some embodiments, amplification conditions include a plurality of cycles wherein steps of annealing, extending and separating are repeated. Typically, amplification conditions include cations such as Mg⁺⁺ or Mn⁺⁺ (e.g., MgCl₂, etc) and can also optionally include various modifiers of ionic strength.

[0015] As used herein, "target sequence" "target nucleic acid sequence" or "target sequence of interest" and derivatives, refers generally to any single or double-stranded nucleic acid sequence that can be amplified or synthesized according to the disclosure, including any nucleic acid sequence suspected or expected to be present in a sample. In some embodiments, the target sequence is present in double-stranded form and includes at least a portion of the particular nucleotide sequence to be amplified or synthesized, or its complement, prior to the addition of target-specific primers or appended adaptors. Target sequences can include the nucleic acids to which primers useful in the amplification or synthesis reaction can hybridize prior to extension by a polymerase. In some embodiments, the term refers to a nucleic acid sequence whose sequence identity, ordering or location of nucleotides is determined by one or more of the methods of the disclosure.

[0016] The term "portion" and its variants, as used herein, when used in reference to a given nucleic acid molecule, for example a primer or a template nucleic acid molecule, comprises any number of contiguous nucleotides within the length of the nucleic acid molecule, including the partial or entire length of the nucleic acid molecule.

[0017] As used herein, "contacting" and its derivatives, when used in reference to two or more components, refers generally to any process whereby the approach, proximity, mixture or commingling of the referenced components is promoted or achieved without necessarily requiring physical contact of such components, and includes mixing of solutions containing any one or more of the referenced components with each other. The referenced components may be contacted in any particular order or combination and the particular order of recitation of components is not limiting. For example, "contacting A with B and C" encompasses embodiments where A is first contacted with B then C, as well as embodiments where C is contacted with A then B, as well as embodiments where a mixture of A and C is contacted with B, and the like. Furthermore, such contacting does not necessarily require that the end result of the contacting process be a mixture including all of the referenced components, as long as at some point during the contacting process all of the referenced components are simultaneously present or simultaneously included in the same mixture or solution. For example, "contacting A with B and C" can include embodiments wherein C is first contacted with A to form a first mixture, which first mixture is then contacted with B to form a second mixture, following which C is removed from the second mixture; optionally A can then also be removed, leaving only B. Where one or more of the referenced components to be contacted includes a plurality (e.g., "contacting a target sequence with a plurality of target-specific primers and a polymerase"), then each member of the plurality can be viewed as an individual component of the contacting process, such that the contacting can include contacting of any one or more members of the plurality with any other member of the plurality and/or with any other referenced component (e.g., some but not all of the plurality of target specific primers can be contacted with a target sequence, then a polymerase, and then with other members of the plurality of target-specific primers) in any order or combination.

[0018] As used herein, the term "primer" and its derivatives refer generally to any polynucleotide that can hybridize to a target sequence of interest. In some embodiments, the primer can also serve to prime nucleic acid synthesis. Typically, a primer functions as a substrate onto which nucleotides can be polymerized by a polymerase; in some embodiments, however, a primer can become incorporated into a synthesized nucleic acid strand and provide a site to which another primer can hybridize to prime synthesis of a new strand that is complementary to the synthesized nucleic acid molecule. A primer may be comprised of any combination of nucleotides or analogs thereof, which may be optionally linked to form a linear polymer of any suitable length. In some embodiments, a primer is a single-stranded oligonucleotide or polynucleotide. (For purposes of this disclosure, the terms 'polynucleotide" and "oligonucleotide" are used interchangeably herein and do not necessarily indicate any difference in length between the two). In some embodiments, a primer is double-stranded. If double stranded, a primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is an oligodeoxyribonucleotide. A primer must be sufficiently long to prime the synthesis of extension products. Lengths of the primers will depend on many factors, including temperature, source of primer and the use of the method. In some embodiments, a primer acts as a point of initiation for amplification or synthesis when exposed to amplification or synthesis conditions; such amplification or synthesis can occur in a template-dependent fashion and optionally results in formation of a primer extension product that is complementary to at least a portion of the target sequence. Exemplary amplification or synthesis conditions can include contacting the primer with a polynucleotide template (e.g., a template including a target sequence), nucleotides and an inducing agent such as a polymerase at a suitable temperature and pH to induce polymerization of nucleotides onto an end of the target-specific primer. If double-stranded, the primer can optionally be treated to separate its strands before being used to prepare primer extension products. In some embodiments, the primer is an oligodeoxyribonucleotide or an oligoribonucleotide. In some embodiments, the primer can include one or more nucleotide analogs. The exact length and/or composition, including sequence, of the target-specific primer can influence many properties, including melting temperature (Tm), GC content, formation of secondary structures, repeat nucleotide motifs, length of predicted primer extension products, extent of coverage across a nucleic acid molecule of interest, number of primers present in a single amplification or synthesis reaction, presence of nucleotide analogs or modified nucleotides within the primers, and the like. In some embodiments, a primer can be paired with a compatible primer within an amplification or synthesis reaction to form a primer pair consisting or a forward primer and a reverse primer. In some embodiments, the forward primer of the primer pair includes a sequence that is substantially complementary to at least a portion of a strand of a nucleic acid molecule, and the reverse primer of the primer of the primer pair includes a sequence that is substantially identical to at least of portion of the strand. In some embodiments, the forward primer and the reverse primer are capable of hybridizing to opposite strands of a nucleic acid duplex. Optionally, the forward primer primes synthesis of a first nucleic acid strand, and the reverse primer primes synthesis of a second nucleic acid strand, wherein the first and second strands are substantially complementary to each other, or can hybridize to form a double-stranded nucleic acid molecule. In some embodiments, one end of an amplification or synthesis product is defined by the forward primer and the other end of the amplification or synthesis product is defined by the reverse primer. In some embodiments, where the amplification or synthesis of lengthy primer extension products is required, such as amplifying an exon, coding region, or gene, several primer pairs can be created than span the desired length to enable sufficient amplification of the region. In some embodiments, a primer can include one or more cleavable groups. In some embodiments, primer lengths are in the range of about 10 to about 60 nucleotides, about 12 to about 50 nucleotides and about 15 to about 40 nucleotides in length. Typically, a primer is capable of hybridizing to a corresponding target sequence and undergoing primer extension when exposed to amplification conditions in the presence of dNTPS and a polymerase. In some instances, the particular nucleotide sequence or a portion of the primer is known at the outset of the amplification reaction or can be determined by one or more of the methods disclosed herein. In some embodiments, the primer includes one or more cleavable groups at one or more locations within the primer.

[0019] As used herein, "target-specific primer" and its derivatives, refers generally to a single stranded or double-stranded polynucleotide, typically an oligonucleotide, that includes at least one sequence that is at least 50% complementary, typically at least 75% complementary or at least 85% complementary, more typically at least 90% complementary, more typically at least 95% complementary, more typically at least 98% or at least 99% complementary, or identical, to at least a portion of a nucleic acid molecule that includes a target sequence. In such instances, the target-specific primer and target sequence are described as "corresponding" to each other. In some embodiments, the target-specific primer is capable of hybridizing to at least a portion of its corresponding target sequence (or to a complement of the target sequence); such hybridization can optionally be performed under standard hybridization conditions or under stringent hybridization conditions. In some embodiments, the target-specific primer is not capable of hybridizing to the target sequence, or to its complement, but is capable of hybridizing to a portion of a nucleic acid strand including the target sequence, or to its complement. In some embodiments, the target-specific primer includes at least one sequence that is at least 75% complementary, typically at least 85% complementary, more typically at least 90% complementary, more typically at least 95% complementary, more typically at least 98% complementary, or more typically at least 99% complementary, to at least a portion of the target sequence itself; in other embodiments, the target-specific primer includes at least one sequence that is at least 75% complementary, typically at least 85% complementary, more typically at least 90% complementary, more typically at least 95% complementary, more typically at least 98% complementary, or more typically at least 99% complementary, to at least a portion of the nucleic acid molecule other than the target sequence. In some embodiments, the target-specific primer is substantially non-complementary to other target sequences present in the sample; optionally, the target-specific primer is substantially non-complementary to other nucleic acid molecules present in the sample. In some embodiments, nucleic acid molecules present in the sample that do not include or correspond to a target sequence (or to a complement of the target sequence) are referred to as "non-specific" sequences or "non-specific nucleic acids". In some embodiments, the target-specific primer is designed to include a nucleotide sequence that is substantially complementary to at least a portion of its corresponding target sequence. In some embodiments, a target-specific primer is at least 95% complementary, or at least 99% complementary, or identical, across its entire length to at least a portion of a nucleic acid molecule that includes its corresponding target sequence. In some embodiments, a target-specific primer can be at least 90%, at least 95% complementary, at least 98% complementary or at least 99% complementary, or identical, across its entire length to at least a portion of its corresponding target sequence. In some embodiments, a forward target-specific primer and a reverse target-specific primer define a target-specific primer pair that can be used to amplify the target sequence via template-dependent primer extension. Typically, each primer of a target-specific primer pair includes at least one sequence that is substantially complementary to at least a portion of a nucleic acid molecule including a corresponding target sequence but that is less than 50% complementary to at least one other target sequence in the sample. In some embodiments, amplification can be performed using multiple target-specific primer pairs in a single amplification reaction, wherein each primer pair includes a forward target-specific primer and a reverse target-specific primer, each including at least one sequence that substantially complementary or substantially identical to a corresponding target sequence in the sample, and each primer pair having a different corresponding target sequence. In some embodiments, the target-specific primer can be substantially non-complementary at its 3' end or its 5' end to any other target-specific primer present in an amplification reaction. In some embodiments, the target-specific primer can include minimal cross hybridization to other target-specific primers in the amplification reaction. In some embodiments, target-specific primers include minimal cross-hybridization to non-specific sequences in the amplification reaction mixture. In some embodiments, the target-specific primers include minimal self-complementarity. In some embodiments, the target-specific primers can include one or more cleavable groups located at the 3' end. In some embodiments, the target-specific primers can include one or more cleavable groups located near or about a central nucleotide of the target-specific primer. In some embodiments, one of more targets-specific primers includes only non-cleavable nucleotides at the 5' end of the target-specific primer. In some embodiments, a target specific primer includes minimal nucleotide sequence overlap at the 3'end or the 5' end of the primer as compared to one or more different target-specific primers, optionally in the same amplification reaction. In some embodiments 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more, target-specific primers in a single reaction mixture include one or more of the above embodiments. In some embodiments, substantially all of the plurality of target-specific primers in a single reaction mixture includes one or more of the above embodiments.

[0020] As used herein, the term "adaptor" denotes a nucleic acid molecule that can be used for manipulation of a polynucleotide of interest. In some embodiments, adaptors are used for amplification of one or more target nucleic acids. In some embodiments, the adaptors are used in reactions for sequencing. In some embodiments, an adaptor has one or more ends that lack a 5' phosphate residue. In some embodiments, an adaptor comprises, consists of, or consist essentially of at least one priming site. Such priming site containing adaptors can be referred to as "primer" adaptors. In some embodiments, the adaptor priming site can be useful in PCR processes. In some embodiments an adaptor includes a nucleic acid sequence that is substantially complementary to the 3' end or the 5' end of at least one target sequences within the sample, referred to herein as a gene specific target sequence, a target specific sequence, or target specific primer. In some embodiments, the adaptor includes nucleic acid sequence that is substantially non-complementary to the 3' end or the 5' end of any target sequence present in the sample. In some embodiments, the adaptor includes single stranded or double-stranded linear oligonucleotide that is not substantially complementary to an target nucleic acid sequence. In some embodiments, the adaptor includes nucleic acid sequence that is substantially non-complementary to at least one, and preferably some or all of the nucleic acid molecules of the sample. In some embodiments, suitable adaptor lengths are in the range of about 10-75 nucleotides, about 12-50 nucleotides and about 15-40 nucleotides in length. Generally, an adaptor can include any combination of nucleotides and/or nucleic acids. In some aspects, adaptors include one or more cleavable groups at one or more locations. In some embodiments, the adaptor includes sequence that is substantially identical, or substantially complementary, to at least a portion of a primer, for example a universal primer. In some embodiments, adaptors include a tag sequence to assist with cataloguing, identification or sequencing. In some embodiments, an adaptor acts as a substrate for amplification of a target sequence, particularly in the presence of a polymerase and dNTPs under suitable temperature and pH.

[0021] As used herein, "polymerase" and its derivatives, generally refers to any enzyme that can catalyze the polymerization of nucleotides (including analogs thereof) into a nucleic acid strand. Typically but not necessarily, such nucleotide polymerization can occur in a template-dependent fashion. Such polymerases can include without limitation naturally occurring polymerases and any subunits and truncations thereof, mutant polymerases, variant polymerases, recombinant, fusion or otherwise engineered polymerases, chemically modified polymerases, synthetic molecules or assemblies, and any analogs, derivatives or fragments thereof that retain the ability to catalyze such polymerization. Optionally, the polymerase can be a mutant polymerase comprising one or more mutations involving the replacement of one or more amino acids with other amino acids, the insertion or deletion of one or more amino acids from the polymerase, or the linkage of parts of two or more polymerases. Typically, the polymerase comprises one or more active sites at which nucleotide binding and/or catalysis of nucleotide polymerization can occur. Some exemplary polymerases include without limitation DNA polymerases and RNA polymerases. The term "polymerase" and its variants, as used herein, also refers to fusion proteins comprising at least two portions linked to each other, where the first portion comprises a peptide that can catalyze the polymerization of nucleotides into a nucleic acid strand and is linked to a second portion that comprises a second polypeptide. In some embodiments, the second polypeptide can include a reporter enzyme or a processivity-enhancing domain. Optionally, the polymerase can possess 5' exonuclease activity or terminal transferase activity. In some embodiments, the polymerase can be optionally reactivated, for example through the use of heat, chemicals or re-addition of new amounts of polymerase into a reaction mixture. In some embodiments, the polymerase can include a hot-start polymerase and/or an aptamer based polymerase that optionally can be reactivated.

[0022] The terms "identity" and "identical" and their variants, as used herein, when used in reference to two or more nucleic acid sequences, refer to similarity in sequence of the two or more sequences (e.g., nucleotide or polypeptide sequences). In the context of two or more homologous sequences, the percent identity or homology of the sequences or subsequences thereof indicates the percentage of all monomeric units (e.g., nucleotides or amino acids) that are the same (i.e., about 70% identity, preferably 75%, 80%, 85%, 90%, 95%, 98% or 99% identity). The percent identity can be over a specified region, when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection. Sequences are said to be "substantially identical" when there is at least 85% identity at the amino acid level or at the nucleotide level. Preferably, the identity exists over a region that is at least about 25, 50, or 100 residues in length, or across the entire length of at least one compared sequence. A typical algorithm for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al, Nuc. Acids Res. 25:3389-3402 (1977). Other methods include the algorithms of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), and Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), etc. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent hybridization conditions.

[0023] The terms "complementary" and "complement" and their variants, as used herein, refer to any two or more nucleic acid sequences (e.g., portions or entireties of template nucleic acid molecules, target sequences and/or primers) that can undergo cumulative base pairing at two or more individual corresponding positions in antiparallel orientation, as in a hybridized duplex. Such base pairing can proceed according to any set of established rules, for example according to Watson-Crick base pairing rules or according to some other base pairing paradigm. Optionally there can be "complete" or "total" complementarity between a first and second nucleic acid sequence where each nucleotide in the first nucleic acid sequence can undergo a stabilizing base pairing interaction with a nucleotide in the corresponding antiparallel position on the second nucleic acid sequence. "Partial" complementarity describes nucleic acid sequences in which at least 20%, but less than 100%, of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, at least 50%, but less than 100%, of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, at least 70%, 80%, 90%, 95% or 98%, but less than 100%, of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. Sequences are said to be "substantially complementary" when at least 85% of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, two complementary or substantially complementary sequences are capable of hybridizing to each other under standard or stringent hybridization conditions. "Non-complementary" describes nucleic acid sequences in which less than 20% of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. Sequences are said to be "substantially non-complementary" when less than 15% of the residues of one nucleic acid sequence are complementary to residues in the other nucleic acid sequence. In some embodiments, two non-complementary or substantially non-complementary sequences cannot hybridize to each other under standard or stringent hybridization conditions. A "mismatch" is present at any position in the two opposed nucleotides are not complementary. Complementary nucleotides include nucleotides that are efficiently incorporated by DNA polymerases opposite each other during DNA replication under physiological conditions. In a typical embodiment, complementary nucleotides can form base pairs with each other, such as the A-T/U and G-C base pairs formed through specific Watson-Crick type hydrogen bonding, or base pairs formed through some other type of base pairing paradigm, between the nucleobases of nucleotides and/or polynucleotides in positions antiparallel to each other. The complementarity of other artificial base pairs can be based on other types of hydrogen bonding and/or hydrophobicity of bases and/or shape complementarity between bases.

[0024] As used herein, "amplified target sequences" and its derivatives, refers generally to a nucleic acid sequence produced by the amplification of/amplifying the target sequences using target-specific primers and the methods provided herein. The amplified target sequences may be either of the same sense (the positive strand produced in the second round and subsequent even-numbered rounds of amplification) or antisense (i.e., the negative strand produced during the first and subsequent odd-numbered rounds of amplification) with respect to the target sequences. For the purposes of this disclosure, amplified target sequences are typically less than 50% complementary to any portion of another amplified target sequence in the reaction.

[0025] As used herein, terms "ligating", "ligation" and derivatives refer generally to the act or process for covalently linking two or more molecules together, for example, covalently linking two or more nucleic acid molecules to each other. In some embodiments, ligation includes joining nicks between adjacent nucleotides of nucleic acids. In some embodiments, ligation includes forming a covalent bond between an end of a first and an end of a second nucleic acid molecule. In some embodiments, for example embodiments wherein the nucleic acid molecules to be ligated include conventional nucleotide residues, the ligation can include forming a covalent bond between a 5' phosphate group of one nucleic acid and a 3' hydroxyl group of a second nucleic acid thereby forming a ligated nucleic acid molecule. In some embodiments, any means for joining nicks or bonding a 5'phosphate to a 3' hydroxyl between adjacent nucleotides can be employed. In an exemplary embodiment, an enzyme such as a ligase can be used.

[0026] As used herein, "ligase" and its derivatives, refers generally to any agent capable of catalyzing the ligation of two substrate molecules. In some embodiments, the ligase includes an enzyme capable of catalyzing the joining of nicks between adjacent nucleotides of a nucleic acid. In some embodiments, a ligase includes an enzyme capable of catalyzing the formation of a covalent bond between a 5' phosphate of one nucleic acid molecule to a 3' hydroxyl of another nucleic acid molecule thereby forming a ligated nucleic acid molecule. Suitable ligases may include, but not limited to, T4 DNA ligase; T7 DNA ligase; Taq DNA ligase, and E. coli DNA ligase.

[0027] As defined herein, a "cleavable group" generally refers to any moiety that once incorporated into a nucleic acid can be cleaved under appropriate conditions. For example, a cleavable group can be incorporated into a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample. In an exemplary embodiment, a target-specific primer can include a cleavable group that becomes incorporated into the amplified product and is subsequently cleaved after amplification, thereby removing a portion, or all, of the target-specific primer from the amplified product. The cleavable group can be cleaved or otherwise removed from a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample by any acceptable means. For example, a cleavable group can be removed from a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample by enzymatic, thermal, photo-oxidative or chemical treatment. In one aspect, a cleavable group can include a nucleobase that is not naturally occurring. For example, an oligodeoxyribonucleotide can include one or more RNA nucleobases, such as uracil that can be removed by a uracil glycosylase. In some embodiments, a cleavable group can include one or more modified nucleobases (such as 7-methylguanine, 8-oxo-guanine, xanthine, hypoxanthine, 5,6-dihydrouracil or 5-methylcytosine) or one or more modified nucleosides (i.e., 7-methylguanosine, 8-oxo-deoxyguanosine, xanthosine, inosine, dihydrouridine or 5-methylcytidine). The modified nucleobases or nucleotides can be removed from the nucleic acid by enzymatic, chemical or thermal means. In one embodiment, a cleavable group can include a moiety that can be removed from a primer after amplification (or synthesis) upon exposure to ultraviolet light (i.e., bromodeoxyuridine). In another embodiment, a cleavable group can include methylated cytosine. Typically, methylated cytosine can be cleaved from a primer for example, after induction of amplification (or synthesis), upon sodium bisulfite treatment. In some embodiments, a cleavable moiety can include a restriction site. For example, a primer or target sequence can include a nucleic acid sequence that is specific to one or more restriction enzymes, and following amplification (or synthesis), the primer or target sequence can be treated with the one or more restriction enzymes such that the cleavable group is removed. Typically, one or more cleavable groups can be included at one or more locations with a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample.

[0028] As used herein, "digestion", "digestion step" and its derivatives, generally refers to any process by which a cleavable group is cleaved or otherwise removed from a target-specific primer, an amplified sequence, an adaptor or a nucleic acid molecule of the sample. In some embodiments, the digestion step involves a chemical, thermal, photo-oxidative or digestive process.

[0029] As used herein, the term "hybridization" is consistent with its use in the art, and generally refers to the process whereby two nucleic acid molecules undergo base pairing interactions. Two nucleic acid molecule molecules are said to be hybridized when any portion of one nucleic acid molecule is base paired with any portion of the other nucleic acid molecule; it is not necessarily required that the two nucleic acid molecules be hybridized across their entire respective lengths and in some embodiments, at least one of the nucleic acid molecules can include portions that are not hybridized to the other nucleic acid molecule. The phrase "hybridizing under stringent conditions" and its variants refers generally to conditions under which hybridization of a target-specific primer to a target sequence occurs in the presence of high hybridization temperature and low ionic strength. As used herein, the phrase "standard hybridization conditions" and its variants refers generally to conditions under which hybridization of a primer to an oligonucleotide (i.e., a target sequence), occurs in the presence of low hybridization temperature and high ionic strength. In one exemplary embodiment, standard hybridization conditions include an aqueous environment containing about 100 mm magnesium sulfate, about 500 mM Tris-sulfate at pH 8.9, and about 200 mM ammonium sulfate at about 50-55°C., or equivalents thereof.

[0030] As used herein, the term "end" and its variants, when used in reference to a nucleic acid molecule, for example a target sequence or amplified target sequence, can include the terminal 30 nucleotides, the terminal 20 and even more typically the terminal 15 nucleotides of the nucleic acid molecule. A linear nucleic acid molecule comprised of linked series of contiguous nucleotides typically includes at least two ends. In some embodiments, one end of the nucleic acid molecule can include a 3' hydroxyl group or its equivalent, and can be referred to as the "3' end" and its derivatives. Optionally, the 3' end includes a 3' hydroxyl group that is not linked to a 5' phosphate group of a mononucleotide pentose ring. Typically, the 3' end includes one or more 5' linked nucleotides located adjacent to the nucleotide including the unlinked 3' hydroxyl group, typically the 30 nucleotides located adjacent to the 3' hydroxyl, typically the terminal 20 and even more typically the terminal 15 nucleotides. Generally, the one or more linked nucleotides can be represented as a percentage of the nucleotides present in the oligonucleotide or can be provided as a number of linked nucleotides adjacent to the unlinked 3' hydroxyl. For example, the 3' end can include less than 50% of the nucleotide length of the oligonucleotide. In some embodiments, the 3' end does not include any unlinked 3' hydroxyl group but can include any moiety capable of serving as a site for attachment of nucleotides via primer extension and/or nucleotide polymerization. In some embodiments, the term "3' end" for example when referring to a target-specific primer, can include the terminal 10 nucleotides, the terminal 5 nucleotides, the terminal 4, 3, 2 or fewer nucleotides at the 3'end. In some embodiments, the term "3' end" when referring to a target-specific primer can include nucleotides located at nucleotide positions 10 or fewer from the 3' terminus. As used herein, "5' end", and its derivatives, generally refers to an end of a nucleic acid molecule, for example a target sequence or amplified target sequence, which includes a free 5' phosphate group or its equivalent. In some embodiments, the 5' end includes a 5' phosphate group that is not linked to a 3' hydroxyl of a neighboring mononucleotide pentose ring. Typically, the 5' end includes to one or more linked nucleotides located adjacent to the 5' phosphate, typically the 30 nucleotides located adjacent to the nucleotide including the 5' phosphate group, typically the terminal 20 and even more typically the terminal 15 nucleotides. Generally, the one or more linked nucleotides can be represented as a percentage of the nucleotides present in the oligonucleotide or can be provided as a number of linked nucleotides adjacent to the 5' phosphate. For example, the 5' end can be less than 50% of the nucleotide length of an oligonucleotide. In another exemplary embodiment, the 5' end can include about 15 nucleotides adjacent to the nucleotide including the terminal 5' phosphate. In some embodiments, the 5' end does not include any unlinked 5' phosphate group but can include any moiety capable of serving as a site of attachment to a 3' hydroxyl group, or to the 3'end of another nucleic acid molecule. In some embodiments, the term "5' end" for example when referring to a target-specific primer, can include the terminal 10 nucleotides, the terminal 5 nucleotides, the terminal 4, 3, 2 or fewer nucleotides at the 5'end. In some embodiments, the term "5' end" when referring to a target-specific primer can include nucleotides located at positions 10 or fewer from the 5' terminus. In some embodiments, the 5' end of a target-specific primer can include only non-cleavable nucleotides, for example nucleotides that do not contain one or more cleavable groups as disclosed herein, or a cleavable nucleotide as would be readily determined by one of ordinary skill in the art. A "first end" and a "second end" of a polynucleotide refer to the 5' end or the 3'end of the polynucleotide. Either the first end or second end of a polynucleotide can be the 5' end or the 3' end of the polynucleotide; the terms "first" and "second" are not meant to denote that the end is specifically the 5' end or the 3' end.

[0031] As used herein "tag," "barcode," "unique tag" or "tag sequence" and its derivatives, refers generally to a unique short (6-14 nucleotide) nucleic acid sequence within an adaptor or primer that can act as a 'key' to distinguish or separate a plurality of amplified target sequences in a sample. For the purposes of this disclosure, a barcode or unique tag sequence is incorporated into the nucleotide sequence of an adaptor or primer. As used herein, "barcode sequence" denotes a nucleic acid fixed sequence that is sufficient to allow for the identification of a sample or source of nucleic acid sequences of interest. A barcode sequence can be, but need not be, a small section of the original nucleic acid sequence on which the identification is to be based. In some embodiments a barcode is 5-20 nucleic acids long. In some embodiments, the barcode is comprised of analog nucleotides, such as L-DNA, LNA, PNA, etc. As used herein, "unique tag sequence" denotes a nucleic acid sequence having at least one random sequence and at least one fixed sequence. A unique tag sequence, alone or in conjunction with a second unique tag sequence, is sufficient to allow for the identification of a single target nucleic acid molecule in a sample. A unique tag sequence can, but need not, comprise a small section of the original target nucleic acid sequence. In some embodiments a unique tag sequence is 2-50 nucleotides or base-pairs, or 2-25 nucleotides or base-pairs, or 2-10 nucleotides or base-pairs in length. A unique tag sequence can comprise at least one random sequence interspersed with a fixed sequence.

[0032] As used herein, "comparable maximal minimum melting temperatures" and its derivatives, refers generally to the melting temperature (Tm) of each nucleic acid fragment for a single adaptor or target-specific primer after digestion of a cleavable groups. The hybridization temperature of each nucleic acid fragment generated by an adaptor or target-specific primer is compared to determine the maximal minimum temperature required preventing hybridization of a nucleic acid sequence from the target-specific primer or adaptor or fragment or portion thereof to a respective target sequence. Once the maximal hybridization temperature is known, it is possible to manipulate the adaptor or target-specific primer, for example by moving the location of one or more cleavable group(s) along the length of the primer, to achieve a comparable maximal minimum melting temperature with respect to each nucleic acid fragment to thereby optimize digestion and repair steps of library preparation.

[0033] As used herein, "addition only" and its derivatives, refers generally to a series of steps in which reagents and components are added to a first or single reaction mixture. Typically, the series of steps excludes the removal of the reaction mixture from a first vessel to a second vessel in order to complete the series of steps. Generally, an addition only process excludes the manipulation of the reaction mixture outside the vessel containing the reaction mixture. Typically, an addition-only process is amenable to automation and high-throughput.

[0034] As used herein, "polymerizing conditions" and its derivatives, refers generally to conditions suitable for nucleotide polymerization. In typical embodiments, such nucleotide polymerization is catalyzed by a polymerase. In some embodiments, polymerizing conditions include conditions for primer extension, optionally in a template-dependent manner, resulting in the generation of a synthesized nucleic acid sequence. In some embodiments, the polymerizing conditions include polymerase chain reaction (PCR). Typically, the polymerizing conditions include use of a reaction mixture that is sufficient to synthesize nucleic acids and includes a polymerase and nucleotides. The polymerizing conditions can include conditions for annealing of a target-specific primer to a target sequence and extension of the primer in a template dependent manner in the presence of a polymerase. In some embodiments, polymerizing conditions can be practiced using thermocycling. Additionally, polymerizing conditions can include a plurality of cycles where the steps of annealing, extending, and separating the two nucleic strands are repeated. Typically, the polymerizing conditions include a cation such as MgCl₂. Generally, polymerization of one or more nucleotides to form a nucleic acid strand includes that the nucleotides be linked to each other via phosphodiester bonds, however, alternative linkages may be possible in the context of particular nucleotide analogs.

[0035] As used herein, the term "nucleic acid" refers to natural nucleic acids, artificial nucleic acids, analogs thereof, or combinations thereof, including polynucleotides and oligonucleotides. As used herein, the terms "polynucleotide" and "oligonucleotide" are used interchangeably and mean single-stranded and double-stranded polymers of nucleotides including, but not limited to, 2'-deoxyribonucleotides (nucleic acid) and ribonucleotides (RNA) linked by internucleotide phosphodiester bond linkages, e.g. 3'-5' and 2'-5', inverted linkages, e.g. 3'-3' and 5'-5', branched structures, or analog nucleic acids. Polynucleotides have associated counter ions, such as H⁺, NH₄⁺, trialkylammonium, Mg²⁺, Na⁺ and the like. An oligonucleotide can be composed entirely of deoxyribonucleotides, entirely of ribonucleotides, or chimeric mixtures thereof. Oligonucleotides can be comprised of nucleobase and sugar analogs. Polynucleotides typically range in size from a few monomeric units, e.g. 5-40, when they are more commonly frequently referred to in the art as oligonucleotides, to several thousands of monomeric nucleotide units, when they are more commonly referred to in the art as polynucleotides; for purposes of this disclosure, however, both oligonucleotides and polynucleotides may be of any suitable length. Unless denoted otherwise, whenever a oligonucleotide sequence is represented, it will be understood that the nucleotides are in 5' to 3' order from left to right and that "A" denotes deoxyadenosine, "C" denotes deoxycytidine, "G" denotes deoxyguanosine, "T" denotes thymidine, and "U' denotes deoxyuridine. As discussed herein and known in the art, oligonucleotides and polynucleotides are said to have "5' ends" and "3' ends" because mononucleotides are typically reacted to form oligonucleotides via attachment of the 5' phosphate or equivalent group of one nucleotide to the 3' hydroxyl or equivalent group of its neighboring nucleotide, optionally via a phosphodiester or other suitable linkage.

[0036] As used herein, the term "polymerase chain reaction" ("PCR") refers to the method of K. B. Mullis U.S. Pat. Nos. 4,683,195 and 4,683,202, hereby incorporated by reference, which describe a method for increasing the concentration of a segment of a polynucleotide of interest in a mixture of genomic DNA without cloning or purification. This process for amplifying the polynucleotide of interest consists of introducing a large excess of two oligonucleotide primers to the DNA mixture containing the desired polynucleotide of interest, followed by a precise sequence of thermal cycling in the presence of a DNA polymerase. The two primers are complementary to their respective strands of the double stranded polynucleotide of interest. To effect amplification, the mixture is denatured and the primers then annealed to their complementary sequences within the polynucleotide of interest molecule. Following annealing, the primers are extended with a polymerase to form a new pair of complementary strands. The steps of denaturation, primer annealing and polymerase extension can be repeated many times (i.e., denaturation, annealing and extension constitute one "cycle"; there can be numerous "cycles") to obtain a high concentration of an amplified segment of the desired polynucleotide of interest. The length of the amplified segment of the desired polynucleotide of interest (amplicon) is determined by the relative positions of the primers with respect to each other, and therefore, this length is a controllable parameter. By virtue of repeating the process, the method is referred to as the "polymerase chain reaction" (hereinafter "PCR"). Because the desired amplified segments of the polynucleotide of interest become the predominant nucleic acid sequences (in terms of concentration) in the mixture, they are said to be "PCR amplified". As defined herein, target nucleic acid molecules within a sample including a plurality of target nucleic acid molecules are amplified via PCR. In a modification to the method discussed above, the target nucleic acid molecules can be PCR amplified using a plurality of different primer pairs, in some cases, one or more primer pairs per target nucleic acid molecule of interest, thereby forming a multiplex PCR reaction. Using multiplex PCR, it is possible to simultaneously amplify multiple nucleic acid molecules of interest from a sample to form amplified target sequences. It is also possible to detect the amplified target sequences by several different methodologies (e.g., quantitation with a bioanalyzer or qPCR, hybridization with a labeled probe; incorporation of biotinylated primers followed by avidin-enzyme conjugate detection; incorporation of ³²P-labeled deoxynucleotide triphosphates, such as dCTP or dATP, into the amplified target sequence). Any oligonucleotide sequence can be amplified with the appropriate set of primers, thereby allowing for the amplification of target nucleic acid molecules from genomic DNA, cDNA, formalin-fixed paraffin-embedded DNA, fine-needle biopsies and various other sources. In particular, the amplified target sequences created by the multiplex PCR process as disclosed herein, are themselves efficient substrates for subsequent PCR amplification or various downstream assays or manipulations.

[0037] As defined herein "multiplex amplification" refers to selective and non-random amplification of two or more target sequences within a sample using at least one target-specific primer. In some embodiments, multiplex amplification is performed such that some or all of the target sequences are amplified within a single reaction vessel. The "plexy" or "plex" of a given multiplex amplification refers generally to the number of different target-specific sequences that are amplified during that single multiplex amplification. In some embodiments, the plexy can be about 12-plex, 24-plex, 48-plex, 96-plex, 192-plex, 384-plex, 768-plex, 1536-plex, 3072-plex, 6144-plex or higher.

[0038] Methods of Preparing Nucleic Acid Libraries

[0039] Provided methods of the invention comprise efficient procedures which enable rapid preparation of highly multiplexed libraries suitable for downstream analysis. See FIG. 1. The methods optionally allow for incorporation of one or more unique tag sequences, if so desired. Certain methods comprise streamlined, addition-only procedures conveying highly rapid library generation.

[0040] In one aspect of the invention, methods for preparing a library of target nucleic acid sequences are provided. In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

[0041] In one aspect of the invention, methods for preparing a tagged library of target nucleic acid sequences are provided. In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and the cleavable moieties are included flanking either end of the tag sequence.

[0042] In certain embodiments, the comparable maximal minimum melting temperature of each universal sequence is higher than the comparable maximal minimum melting temperature of each target nucleic acid sequence and each tag sequence present in an adaptor.

[0043] In some embodiments, each of the adaptors comprise unique tag sequences as further described herein and each further comprise cleavable groups flanking either end of the tag sequence in each adaptor. In some embodiments wherein unique taq sequences are employed, each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In certain embodiments each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences.

[0044] In some embodiments, methods comprise contacting the plurality of gapped polynucleotide products with digestion and repair reagents simultaneously. In some embodiments, methods comprise contacting the plurality of gapped polynucleotide products sequentially with the digestion then repair reagents.

[0045] A digestion reagent useful in the methods provided herein comprises any reagent capable of cleaving the cleavable site present in adaptors, and in some embodiments includes, but is not limited to, one or a combination of uracil DNA glycosylase (UDG) . apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta.

[0046] A repair reagent useful in the methods provided herein comprises any reagent capable of repair of the gapped amplicons, and in some embodiments includes, but is not limited to, any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase.

[0047] Thus, in certain embodiments, a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG) . apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG),apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase.

[0048] In some embodiments, methods comprise the digestion and repair steps carried out in a single step. In other embodiments, methods comprise the digestion and repair of steps carried out in a temporally separate manner at different temperatures.

[0049] In some embodiments methods of the invention are carried out wherein one or more of the method steps is conducted in manual mode. In particular embodiments, methods of the invention are carried out wherein each of the method steps is conducted manually. In some embodiments methods of the invention are carried out wherein one or more of the method steps is conducted in an automated mode. In particular embodiments, methods of the invention are carried wherein each of the method steps is automated. In some embodiments methods of the invention are carried out wherein one or more of the method steps is conducted in a combination of manual and automated modes.

[0050] In some embodiments, methods of the invention comprise at least one purification step. For example, in certain embodiments a purification step is carried out only after the second amplification of repaired amplicons. In some embodiments two purification steps are utilized, wherein a first purification step is carried out after the digestion and repair and a second purification step is carried out after the second amplification of repaired amplicons.

[0051] In some embodiments a purification step comprises conducting a solid phase adherence reaction, solid phase immobilization reaction or gel electrophoresis. In certain embodiments a purification step comprises separation conducted using Solid Phase Reversible Immobilization (SPRI) beads. In particular embodiments a purification step comprises separation conducted using SPRI beads wherein the SPRI beads comprise paramagnetic beads.

[0052] In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, then purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

[0053] In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, and purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and cleavable moieties are included in the flanking either end of the tag sequence.

[0054] In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, then purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence. In some embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG),apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase.

[0055] In some embodiments, methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons, and purifying repaired amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences; and then purifying resulting library. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and cleavable moieties are included in the flanking either end of the tag sequence. In some embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG) . apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG),apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase.

[0056] In certain embodiments methods of the invention are carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries. For example, in one embodiment, methods for preparing a library of target nucleic acid sequences comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library. In certain embodiments the purification comprises a single or repeated separating step that is carried out following production of the library following the second amplification; and wherein the other method steps are conducted in a single reaction vessel without requisite transferring of a portion (aliquot) of any of the products generated in steps to another reaction vessel. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

[0057] In another embodiment, methods for preparing a tagged library of target nucleic acid sequences are provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library. In certain embodiments the purification comprises a single or repeated separating step; and wherein the other method steps are optionally conducted in a single reaction vessel without requisite transferring of a portion of any of the products generated in steps to another reaction vessel. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and the cleavable moieties are included flanking either end of the tag sequence.

[0058] , In one embodiment, methods for preparing a library of target nucleic acid sequences comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicon; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library.

[0059] In some embodiments a digestion reagent comprises any one or any combination of: uracil DNA glycosylase (UDG). AP endonuclease (APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase, Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In certain embodiments a digestion reagent comprises any one or any combination of: uracil DNA glycosylase (UDG). AP endonuclease (APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase, Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta wherein the digestion reagent lacks formamidopyrimidine [fapy]-DNA glycosylase (fpg).

[0060] In some embodiments a digestion reagent comprises a single-stranded DNA exonuclease that degrades in a 5'-3' direction. In some embodiments a cleavage reagent comprises a single-stranded DNA exonuclease that degrades abasic sites. In some embodiments herein the digestions reagent comprises an RecJf exonuclease. In particular embodiments a digestion reagent comprises APE1 and RecJf, wherein the cleavage reagent comprises an apurinic/apyrimidinic endonuclease. In certain embodiments the digestion reagent comprises an AP endonuclease (APE1).

[0061] In some embodiments a repair reagent comprises at least one DNA polymerase; wherein the gap-filling reagent comprises: any one or any combination of: Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase and/or SuperFi U DNA polymerase. In some embodiments a repair reagent further comprises a plurality of nucleotides.

[0062] In some embodiment a repair reagent comprises an ATP-dependent or an ATP-independent ligase; wherein the repair reagent comprises any one or any combination of: E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase. , 9°N DNA ligase

[0063] In certain embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG). apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments a purification comprises a single or repeated separating step that is carried out following production of the library following the second amplification; and wherein method steps are conducted in a single reaction vessel without requisite transferring of a portion of any of the products generated in steps to another reaction vessel until a first purification. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and optionally one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. In some embodiments where an optional tag sequence is included in at least one adaptor, the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

[0064] In another embodiment, methods for preparing a tagged library of target nucleic acid sequences are provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, thereby producing gapped, double stranded amplicons. The methods further comprise repairing the partially digested target amplicons; then amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences, and purifying the resulting library. In certain embodiments a digestion and repair reagent comprises any one or a combination of one or a combination of uracil DNA glycosylase (UDG) . apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta; and any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments, a digestion and repair reagent comprises any one or a combination of uracil DNA glycosylase (UDG),apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, T7 DNA ligase. In certain embodiments the purification comprises a single or repeated separating step that is carried out following production of the library following the second amplification; and wherein steps the other method steps are conducted in a single reaction vessel without requisite transferring of a portion (aliquot) of any of the products generated in steps to another reaction vessel. Each of the plurality of adaptors used in the methods herein comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and one or more tag sequences. At least two and up to one hundred thousand target specific adaptor pairs are included in the provided methods, wherein the target nucleic acid sequence of each adaptor includes at least one cleavable moiety, the universal handle sequence does not include the cleavable moiety, and the cleavable moieties are included flanking either end of the tag sequence.

[0065] In some embodiments, adaptor-dimer byproducts resulting from the first amplification of step of the methods are largely removed from the resulting library. In certain embodiments the enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In particular embodiments adaptor dimer byproducts are eliminated.

[0066] In some embodiments, the library is prepared in less than 4 hours. In some embodiments, the library is prepared, enriched and sequenced in less than 3 hours. In some embodiments, the library is prepared, enriched and sequenced in 2 to 3 hours. In some embodiments, the library is prepared in approximately 2.5 hours. In some embodiments, the library is prepared in approximately 2.75 hours. In some embodiments, the library is prepared in approximately 3 hours.

Compositions

[0067] Additional aspects of the invention comprise composition comprising a plurality of nucleic acid adaptors, as well as library compositions prepared according to the methods of the invention. Provided compositions are useful in conjunction with the methods described herein as well as for additional analysis and applications known in the art.

[0068] Thus, provided are composition comprising a plurality of nucleic acid adaptors, wherein each of the plurality of adaptors comprises a 5' universal handle sequence, optionally one or more tag sequences, and a 3' target nucleic acid sequence wherein each adaptor comprises a cleavable moiety, wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, and when tag sequences are present cleavable moieties are included flanking either end of the tag sequence and wherein the universal handle sequence does not include the cleavable moiety. At least two and up to one hundred thousand target specific adaptor pairs are included in provided compositions. Provided composition allow for rapid production of highly multiplexed targeted libraries.

[0069] In some embodiments, provided compositions comprise plurality of nucleic acid adaptors, wherein each of the plurality of adaptors comprise a 5' universal handle sequence, one or more tag sequences, and a 3' target nucleic acid sequence wherein each adaptor comprises a cleavable moiety; wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety. At least two and up to one hundred thousand target specific adaptor pairs are included in provided compositions. Provided composition allow for rapid production of highly multiplexed, tagged, targeted libraries.

[0070] Primer/adaptor compositions may be single stranded or double stranded. In some embodiments adaptor compositions comprise are single stranded adaptors. In some embodiments adaptor compositions comprise double stranded adaptors. In some embodiments adaptor compositions comprise a mixture of single stranded and double stranded adaptors.

[0071] In some embodiments, compositions include a plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprising a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences wherein the target-specific primer sequence is substantially non-complementary to other target specific primer sequences in the composition. In some embodiments, the composition comprises at least 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 750, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4500, 5000, 5500, 6000, 7000, 8000, 9000, 10000, 11000, or 12000, or more target-specific adaptor pairs. In some embodiments, target-specific adpator pairs comprise about 15 nucleotides to about 40 nucleotides in length, wherein at least one nucleotide is replaced with a cleavable group. In some embodiments the cleavable group is a uridine nucleotide. In some embodiments, the target-specific adaptor pairs are designed to amplify an exon, gene, exome or region of the genome associated with a clinical or pathological condition, e.g., amplification of one or more sites comprising one or more mutations (e.g., driver mutation) associated with a cancer, e.g., lung, colon, breast cancer, etc., or amplification of mutations associated with an inherited disease, e.g., cystic fibrosis, muscular dystrophies, etc. In some embodiments, the target-specific adaptor pairs when hybridized to a target sequence and amplified as provided herein generates a library of adaptor-ligated amplified target sequences that are about 100 to about 600 base pairs in length. In some embodiments, no one adaptor-ligated amplified target sequence is overexpressed in the library by more than 30% as compared to the remainder of other adaptor-ligated amplified target sequences in the library. In some embodiments, an adaptor-ligated amplified target sequence library is substantially homogenous with respect to GC content, amplified target sequence length or melting temperature (Tm) of the respective target sequences.

[0072] In some embodiments, the target-specific primer sequences of adaptor pairs in the compositions of the invention are target-specific sequences that can amplify specific regions of a nucleic acid molecule. In some embodiments, the target-specific adaptors can amplify genomic DNA or cDNA. In some embodiments, target-specific adaptors can amplify mammalian nucleic acid, such as, but not limited to human DNA or RNA, murine DNA or RNA, bovine DNA or RNA, canine DNA or RNA, equine DNA or RNA, or any other mammal of interest. In other embodiments, target specific adaptors include sequences directed to amplify plant nucleic acids of interest. In other embodiments, target specific adaptors include sequences directed to amplify infectious agents, e.g., bacterial and/or viral nucleic acids. In some embodiments, the amount of nucleic acid required for selective amplification is from about 1 ng to 1 microgram. In some embodiments, the amount of nucleic acid required for selective amplification of one or more target sequences is about 1 ng, about 5 ng or about 10 ng. In some embodiments, the amount of nucleic acid required for selective amplification of target sequence is about 10 ng to about 200 ng.

[0073] As described herein, each of the plurality of adaptors comprises a 5' universal handle sequence. In some embodiments a universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In some embodiments the comparable maximal minimum melting temperatures of each adaptor universal handle sequence is higher than the comparable maximal minimum melting temperatures of each target nucleic acid sequence and each tag sequence present in the same adaptor. Preferably, the universal handle sequences of provided adaptors do not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence of interest. In some embodiments a first universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In some embodiments a second universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In certain embodiments first and second universal handle sequences correspond to forward and reverse universal handle sequences and in certain embodiments the same first and second universal handle sequences are included for each of the plurality of target specific adaptor pairs. Such forward and reverse universal handle sequences are targeted in conjunction with universal primers to carry out a second amplification of repaired amplicons in production of libraries according to methods of the invention. In certain embodiments a first 5' universal handle sequence comprises two universal handle sequences(e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence); and a second 5' universal sequence comprises two universal handle sequences (e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence), wherein the 5' first and second universal handle sequences do not exhibit significant hybridization to any portion of a target nucleic acid sequence of interest.

[0074] The structure and properties of universal amplification primers or universal primers are well known to those skilled in the art and can be implemented for utilization in conjunction with provided methods and compositions to adapt to specific analysis platforms. Universal handle sequences of the adaptors provided herein are adapted accordingly to accommodate a preferred universal primer sequences. For example, e.g., as described herein universal P1 and A primers with optional barcode sequences have been described in the art and utilized for sequencing on Ion Torrent sequencing platforms (Ion Xpress^™ Adapters, Thermo Fisher Scientific). Similarly, additional and other universal adaptor/primer sequences described and known in the art (e.g., Illumina universal adaptor/primer sequences can be found,e.g., at https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf; PacBio universal adaptor/primer sequences, can be found, e.g., at https://s3.amazonaws.com/files.pacb.com/pdf/Guide_Pacific_Biosciences_Template_Preparation_an d_Sequencing.pdf; etc.) can be used in conjunction with the methods and compositions provided herein. Suitable universal primers of appropriate nucleotide sequence for use with adaptors of the invention are readily prepared using standard automated nucleic acid synthesis equipment and reagents in routine use in the art. One single type of universal primer or separate types (or even a mixture) of two different universal primers, for example a pair of universal amplification primers suitable for amplification of repaired amplicons in a second amplification are included for use in the methods of the invention. Universal primers optionally include a different tag (barcode) sequence, where the tag (barcode) sequence does not hybridize to the adaptor. Barcode sequences incorporated into amplicons in a second universal amplification can be utilized e.g., for effective identification of sample source.

[0075] In some embodiments adaptors further comprise a unique tag sequence located between the 5' first universal handle sequence and the 3' target-specific sequence, and wherein the unique tag sequence does not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence of interest. In some embodiments the plurality of primer adaptor pairs has 10⁴-10⁹ different tag sequence combinations. Thus in certain embodiments each generated target specific adaptor pair comprises 10⁴-10⁹ different tag sequences. In some embodiments the plurality of primer adaptors comprise each target specific adaptor comprising at least 1 different unique tag sequence and up to 10⁵ different unique tag sequences. In some embodiments the plurality of primer adaptors comprise each target specific adaptor comprising at least 1 different unique tag sequence and up to 10⁵ different unique tag sequences. In certain embodiments each generated target specific amplicon generated comprises at least two and up to 10⁹ different adaptor combinations comprising different tag sequences, each having two different unique tag sequences. In some embodiments the plurality of primer adaptors comprise each target specific adaptor comprising 4096 different tag sequences. In certain embodiments each generated target specific amplicon generated comprises up to 16,777,216 different adaptor combinations comprising different tag sequences, each having two different unique tag sequences.

[0076] In some embodiments individual primer adaptors in the plurality of adaptors include a unique tag sequence (e.g., contained in a tag adaptor) comprising different random tag sequences alternating with fixed tag sequences. In some embodiments, the at least one unique tag sequence comprises a at least one random sequence and at least one fixed sequence, or comprises a random sequence flanked on both sides by a fixed sequence, or comprises a fixed sequence flanked on both sides by a random sequence. In some embodiments a unique tag sequence includes a fixed sequence that is 2-2000 nucleotides or base-pairs in length. In some embodiments a unique tag sequence includes a random sequence that is 2-2000 nucleotides or base-pairs in length.

[0077] In some embodiments, unique tag sequences include a sequence having at least one random sequence interspersed with fixed sequences. In some embodiments, individual tag sequences in a plurality of unique tags have the structure (N)_n(X)_x(M)_m(Y)_y, wherein "N" represents a random tag sequence that is generated from A, G, C, T, U or I, and wherein "n" is 2-10 which represents the nucleotide length of the "N" random tag sequence; wherein "X" represents a fixed tag sequence, and wherein "x" is 2-10 which represents the nucleotide length of the "X" random tag sequence; wherein "M" represents a random tag sequence that is generated from A, G, C, T, U or I, wherein the random tag sequence "M" differs or is the same as the random tag sequence "N", and wherein "m" is 2-10 which represents the nucleotide length of the "M" random tag sequence; and wherein "Y" represents a fixed tag sequence, wherein the fixed tag sequence of "Y" is the same or differs from the fixed tag sequence of "X", and wherein "y" is 2-10 which represents the nucleotide length of the "Y" random tag sequence. In some embodiments, the fixed tag sequence "X" is the same in a plurality of tags. In some embodiments, the fixed tag sequence "X" is different in a plurality of tags. In some embodiments, the fixed tag sequence "Y" is the same in a plurality of tags. In some embodiments, the fixed tag sequence "Y" is different in a plurality of tags. In some embodiments, the fixed tag sequences "(X)_x" and "(Y)_y" within the plurality of adaptors are sequence alignment anchors.

[0078] In some embodiments, the random sequence within a unique tag sequence is represented by "N", and the fixed sequence is represented by "X". Thus, a unique tag sequence is represented by N₁N₂N₃X₁X₂X₃ or by N₁N₂N₃X₁X₂X₃N₄N₅N₆X₄X₅X₆. Optionally, a unique tag sequence can have a random sequence in which some or all of the nucleotide positions are randomly selected from a group consisting of A, G, C, T, U and I. For example, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C, T, U or I, or is selected from a subset of these six different types of nucleotides. Optionally, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C or T. In some embodiments, the first fixed tag sequence "X₁X₂X₃" is the same or different sequence in a plurality of tags. In some embodiments, the second fixed tag sequence "X₄X₅X₆" is the same or different sequence in a plurality of tags. In some embodiments, the first fixed tag sequence "X₁X₂X₃" and the second fixed tag sequence "X₄X₅X₆" within the plurality of adaptors are sequence alignment anchors.

[0079] In some embodiments, a unique tag sequence comprises the sequence 5'-NNNACTNNNTGA-3', where "N" represents a position within the random sequence that is generated randomly from A, G, C or T, the number of possible distinct random tags is calculated to be 4⁶ (or 4^6) is about 4096, and the number of possible different combinations of two unique tags is 4¹² (or 4^12) is about 16.78 million. In some embodiments, the underlined portions of 5'-NNNACTNNNTGA-3' are a sequence alignment anchor.

[0080] In some embodiments, the fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate error-corrected sequencing data. In some embodiments fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate a family of error-corrected sequencing reads.

[0081] Adaptors provided herein comprise at least one cleavable moiety. In some embodiments a cleavable moiety is within the 3' target-specific sequence. In some embodiments a cleavable moiety is at or near the junction between the 5' first universal handle sequence and the 3' target-specific sequence. In some embodiments a cleavable moiety is at or near the junction between the 5' first universal handle sequence and the unique tag sequence, and at or near the junction between the unique tag sequence and the 3' target-specific sequence. The cleavable moiety can be present in a modified nucleotide, nucleoside or nucleobase. In some embodiments, the cleavable moiety can include a nucleobase not naturally occurring in the target sequence of interest.

[0082] In some embodiments the at least one cleavable moiety in the plurality of adaptors is a uracil base, uridine or a deoxyuridine nucleotide. In some embodiments a cleavable moiety is within the 3' target-specific sequence and the junctions between the 5' universal handle sequence and the unique tag sequence and/or the 3'target specific sequence wherein the at least one cleavable moiety in the plurality of adaptors is cleavable with uracil DNA glycosylase (UDG). In some embodiments, a cleavable moiety is cleaved, resulting in a susceptible abasic site, wherein at least one enzyme capable of reacting on the abasic site generates a gap comprising an extendible 3' end. In certain embodiments the resulting gap comprises a 5'-deoxyribose phosphate group. In certain embodiments the resulting gap comprises an extendible 3' end and a 5' ligatable phosphate group.

[0083] In another embodiment, inosine can be incorporated into a DNA-based nucleic acid as a cleavable group. In one exemplary embodiment, EndoV can be used to cleave near the inosine residue. In another exemplary embodiment, the enzyme hAAG can be used to cleave inosine residues from a nucleic acid creating abasic sites.

[0084] Where a cleavable moiety is present, the location of the at least one cleavable moiety in the adaptors does not significantly change the melting temperature (Tm) of any given double-stranded adaptor in the plurality of double-stranded adaptors. The melting temperatures (Tm) of any two given double-stranded adaptors from the plurality of double-stranded adaptors are substantially the same, wherein the melting temperatures (Tm) of any two given double-stranded adaptors does not differ by more than 10 °C of each other. However, within each of the plurality of adaptors, the melting temperatures of sequence regions differs, such that the comparable maximal minimum melting temperature of, for example, the universal handle sequence, is higher than the comparable maximal minimum melting temperatures of either the unique tag sequence and/or the target specific sequence of any adaptor. This localized differential in comparable maximal minimum melting temperatures can be adjusted to optimize digestion and repair of amplicons and ultimately improved effectiveness of the methods provided herein.

[0085] Further provided are compositions comprising a nucleic acid library generated by methods of the invention. Thus, provided are composition comprising a plurality of amplified target nucleic acid amplicons, wherein each of the plurality of amplicons comprises a 5' universal handle sequence, optionally a first unique tag sequences, an intermediate target nucleic acid sequence, optionally a second unique tag sequences and a 3' universal handle sequence . At least two and up to one hundred thousand target specific amplicons are included in provided compositions. Provided compositions include highly multiplexed targeted libraries. In some embodiments, provided compositions comprise a plurality of nucleic acid amplicons, wherein each of the plurality of amplicons comprise a a 5' universal handle sequence, a first unique tag sequences, an intermediate target nucleic acid sequence, a second unique tag sequences and a 3' universal handle sequence . At least two and up to one hundred thousand target specific tagged amplicons are included in provided compositions. Provided compositions include highly multiplexed tagged targeted libraries.

[0086] In some embodiments, library compositions include a plurality of target specific amplicons comprising a multiplex of at least two different target nucleic acid sequences. In some embodiments, the composition comprises at least 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 750, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500, 3750, 4000, 4500, 5000, 5500, 6000, 7000, 8000, 9000, 10000, 11000, or 12000, or more target-specific amplicons. In some embodiments, the target-specific amplicons comprise one or more exon, gene, exome or region of the genome associated with a clinical or pathological condition, e.g., amplicons comprising one or more sites comprising one or more mutations (e.g., driver mutation) associated with a cancer, e.g., lung, colon, breast cancer, etc., or amplicons comprising mutations associated with an inherited disease, e.g., cystic fibrosis, muscular dystrophies, etc. In some embodiments, the target-specific amplicons comprise a library of adaptor-ligated amplicon target sequences that are about 100 to about 750 base pairs in length.

[0087] As described herein, each of the plurality of amplicons comprises a 5' universal handle sequence. In some embodiments a universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. Preferably, the universal handle sequences of provided adaptors do not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence of interest. In some embodiments a first universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In some embodiments a second universal handle sequence comprises any one or any combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence. In certain embodiments first and second universal handle sequences correspond to forward and reverse universal handle sequences and in certain embodiments the same first and second universal handle sequences are included for each of the plurality of target specific amplicons. Such forward and reverse universal handle sequences are targeted in conjunction with universal primers to carry out a second amplification of a preliminary library composition in production of resulting amplified according to methods of the invention. In certain embodiments a first 5' universal handle sequence comprises two universal handle sequences(e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence); and a second 5' universal sequence comprises two universal handle sequences (e.g., a combination of an amplification primer binding sequence, a sequencing primer binding sequence and/or a capture primer binding sequence), wherein the 5' first and second universal handle sequences do not exhibit significant hybridization to any portion of a target nucleic acid sequence of interest.

[0088] The structure and properties of universal amplification primers or universal primers are well known to those skilled in the art and can be implemented for utilization in conjunction with provided methods and compositions to adapt to specific analysis platforms. Universal handle sequences of the adaptors and amplicons provided herein are adapted accordingly to accommodate a preferred universal primer sequences. For example, e.g., as described herein universal P1 and A primers with optional barcode sequences have been described in the art and utilized for sequencing on Ion Torrent sequencing platforms (Ion Xpress^™ Adapters, Thermo Fisher Scientific). Similarly, additional and other universal adaptor/primer sequences described and known in the art (e.g., Illumina universal adaptor/primer sequences can be found,e.g., at https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf; PacBio universal adaptor/primer sequences, can be found, e.g., at https://s3.amazonaws.com/files.pacb.com/pdf/Guide_Pacific_Biosciences_Template_Preparation_an d_Sequencing.pdf; etc.) can be used in conjunction with the methods and compositions provided herein. Suitable universal primers of appropriate nucleotide sequence for use with libraries of the invention are readily prepared using standard automated nucleic acid synthesis equipment and reagents in routine use in the art. One single type or separate types (or even a mixture) of two different universal primers, for example a pair of universal amplification primers suitable for amplification of a preliminary library may be used in production of the libraries of the invention. Universal primers optionally include a tag (barcode) sequence, where the tag (barcode) sequence does not hybridize to adaptor sequence or to target nucleic acid sequences. Barcode sequences incorporated into amplicons in a second universal amplification can be utilized e.g., for effective identification of sample source to thereby generate a barcoded library. Thus provided compositions include highly multiplexed barcoded targeted libraries. Provided compositions also include highly multiplexed barcoded tagged targeted libraries.

[0089] In some embodiments amplicon libraries comprise a unique tag sequence located between the 5' first universal handle sequence and the 3' target-specific sequence, and wherein the unique tag sequence does not exhibit significant complementarity and/or hybridization to any portion of a unique tag sequence and/or target nucleic acid sequence. In some embodiments the plurality of amplicons has 10⁴-10⁹ different tag sequence combinations. Thus in certain embodiments each of the plurality of amplicons in a library comprises 10⁴-10⁹ different tag sequences. In some embodiments each of the plurality of amplicons in a library comprises at least 1 different unique tag sequence and up to 10⁵ different unique tag sequences. In certain embodiments each target specific amplicon in a library comprises at least two and up to 10⁹ different combinations comprising different tag sequences, each having two different unique tag sequences. In some embodiments each of the plurality of amplicons in a library comprise a tag sequence comprising 4096 different tag sequences. In certain embodiments each target specific amplicon of a library comprises up to 16,777,216 different combinations comprising different tag sequences, each having two different unique tag sequences.

[0090] In some embodiments individual amplicons in the plurality of amplicons of a library include a unique tag sequence (e.g., contained in a tag adaptor sequence) comprising different random tag sequences alternating with fixed tag sequences. In some embodiments, the at least one unique tag sequence comprises a at least one random sequence and at least one fixed sequence, or comprises a random sequence flanked on both sides by a fixed sequence, or comprises a fixed sequence flanked on both sides by a random sequence. In some embodiments a unique tag sequence includes a fixed sequence that is 2-2000 nucleotides or base-pairs in length. In some embodiments a unique tag sequence includes a random sequence that is 2-2000 nucleotides or base-pairs in length.

[0091] In some embodiments, unique tag sequences include a sequence having at least one random sequence interspersed with fixed sequences. In some embodiments, individual tag sequences in a plurality of unique tags have the structure (N)_n(X)_x(M)_m(Y)_y, wherein "N" represents a random tag sequence that is generated from A, G, C, T, U or I, and wherein "n" is 2-10 which represents the nucleotide length of the "N" random tag sequence; wherein "X" represents a fixed tag sequence, and wherein "x" is 2-10 which represents the nucleotide length of the "X" random tag sequence; wherein "M" represents a random tag sequence that is generated from A, G, C, T, U or I, wherein the random tag sequence "M" differs or is the same as the random tag sequence "N", and wherein "m" is 2-10 which represents the nucleotide length of the "M" random tag sequence; and wherein "Y" represents a fixed tag sequence, wherein the fixed tag sequence of "Y" is the same or differs from the fixed tag sequence of "X", and wherein "y" is 2-10 which represents the nucleotide length of the "Y" random tag sequence. In some embodiments, the fixed tag sequence "X" is the same in a plurality of tags. In some embodiments, the fixed tag sequence "X" is different in a plurality of tags. In some embodiments, the fixed tag sequence "Y" is the same in a plurality of tags. In some embodiments, the fixed tag sequence "Y" is different in a plurality of tags. In some embodiments, the fixed tag sequences "(X)_x" and "(Y)_y" within the plurality of amplicons are sequence alignment anchors.

[0092] In some embodiments, the random sequence within a unique tag sequence is represented by "N", and the fixed sequence is represented by "X". Thus, a unique tag sequence is represented by N₁N₂N₃X₁X₂X₃ or by N₁N₂N₃X₁X₂X₃N₄N₅N₆X₄X₅X₆. Optionally, a unique tag sequence can have a random sequence in which some or all of the nucleotide positions are randomly selected from a group consisting of A, G, C, T, U and I. For example, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C, T, U or I, or is selected from a subset of these six different types of nucleotides. Optionally, a nucleotide for each position within a random sequence is independently selected from any one of A, G, C or T. In some embodiments, the first fixed tag sequence "X₁X₂X₃" is the same or different sequence in a plurality of tags. In some embodiments, the second fixed tag sequence "X₄X₅X₆" is the same or different sequence in a plurality of tags. In some embodiments, the first fixed tag sequence "X₁X₂X₃" and the second fixed tag sequence "X₄X₅X₆" within the plurality of amplicons are sequence alignment anchors.

[0093] In some embodiments, a unique tag sequence comprises the sequence 5'-NNNACTNNNTGA-3', where "N" represents a position within the random sequence that is generated randomly from A, G, C or T, the number of possible distinct random tags is calculated to be 4⁶ (or 4^6) is about 4096, and the number of possible different combinations of two unique tags is 4¹² (or 4^12) is about 16.78 million. In some embodiments, the underlined portions of 5'-NNNACTNNNTGA-3' are a sequence alignment anchor.

[0094] In some embodiments, the fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate error-corrected sequencing data. In some embodiments fixed sequences within the unique tag sequence is a sequence alignment anchor that can be used to generate a family of error-corrected sequencing reads.

Kits, Systems

[0095] Further provided herein are kits for use in preparing libraries of target nucleic acids using methods of the first or second aspects of the invention. Embodiments of a kit comprise a supply of at least a pair of target specific adaptors as defined herein which are capable of producing a first amplification product; as well as optionally a supply of at least one universal pair of amplification primers capable of annealing to the universal handle(s) of the adaptor and priming synthesis of an amplification product, which amplification product would include a target sequence of interest ligated to a universal sequence. Adaptors and/or primers may be supplied in kits ready for use, or more preferably as concentrates requiring dilution before use, or even in a lyophilized or dried form requiring reconstitution prior to use. In certain embodiments kits further include a supply of a suitable diluent for dilution or reconstitution of the components. Optionally, kits further comprise supplies of reagents, buffers, enzymes, dNTPs, etc., for use in carrying out amplification, digestion, repair, and/or purification in the generation of library as provided herein. Non-limiting examples of such reagents are as described in the Materials and Methods sections of the accompanying Exemplification. Further components which optionally are supplied in the kit include components suitable for purification of libraries prepared using the provided methods._In some embodiments, provided is a kit for generating a target-specific library comprising a plurality of target-specific adaptors having a 5' universal handle sequence, a 3' target specific sequence and a cleavable group, a DNA polymerase, an adaptor, dATP, dCTP, dGTP, dTTP, and a digestion reagent. In some embodiments, the kit further comprises one or more antibodies, a repair reagent, universal primers optionally comprising nucleic acid barcodes, purification solutions or columns.

[0096] Particular features of adaptors for inclusion in kits are as described elsewhere herein in relation to other aspects of the invention. The structure and properties of universal amplification primers are well known to those skilled in the art and can be implemented for utilization in conjunction with provided methods and compositions to adapt to specific analysis platforms (e.g., as described herein universal P1 and A primers have been described in the art and utilized for sequencing on Ion Torrent sequencing platforms). Similarly, additional and other universal adaptor/primer sequences described and known in the art (e.g., Illumina universal adaptor/primer sequences, PacBio universal adaptor/primer sequences, etc.) can be used in conjunction with the methods and compositions provided herein. Suitable primers of appropriate nucleotide sequence for use with adaptors included in the kit is readily prepared using standard automated nucleic acid synthesis equipment and reagents in routine use in the art. A kit may include a supply of one single type of universal primer or separate types (or even a mixture) of two different universal primers, for example a pair of amplification primers suitable for amplification of templates modified with adaptors in a first amplification. A kit may comprise at least a pair of adaptors for first amplification of a sample of interest according to the methods of the invention, plus at least two different amplification primers that optionally carry a different tag (barcode) sequence, where the tag (barcode) sequence does not hybridize to the adaptor. A kit can be used to amplify at least two different samples where each sample is amplified according to methods of the invention separately and a second amplification comprises using a single universal primer having a barcode, and then pooling prepared sample libraries after library preparations. In some embodiments a kit includes different universal primer-pairs for use in second amplification step described herein. In this context the 'universal' primer-pairs may be of substantially identical nucleotide sequence but differ with respect to some other feature or modification.

[0097] Further provided are systems, e.g., systems used to practice methods provided herein, and/or comprising compositions provided herein. In some embodiments, systems facilitate methods carried out in automated mode. In certain embodiments, systems facilitate high throughput mode. In certain embodiments, systems include, e.g., a fluid handling element, a fluid containing element, a heat source and/or heat sink for achieving and maintaining a desired reaction temperature, and/or a robotic element capable of moving components of the system from place to place as needed (e.g., a multiwell plate handling element).

Samples

[0098] As defined herein, "sample" and its derivatives, is used in its broadest sense and includes any specimen, culture and/or the like that is suspected of including a target nucleic acid. In some embodiments, a sample comprises DNA, RNA, chimeric nucleic acid, hybrid nucleic acid, multiplex-forms of nucleic acids or any combination of two or more of the foregoing. In some embodiments a sample useful in conjunction with methods of the invention includes any biological, clinical, surgical, agricultural, atmospheric or aquatic-based specimen containing one or more target nucleic acid of interest. In some embodiments, a sample includes nucleic acid molecules obtained from an animal such as a human or mammalian source. In another embodiment, a sample includes nucleic acid molecules obtained from a non-mammalian source such as a plant, bacteria, virus or fungus. In some embodiments, the source of the nucleic acid molecules may be an archived or extinct sample or species. In some embodiments a sample includes isolated nucleic acid sample prepared, for example, from a source such as genomic DNA, RNA or a prepared sample such as, e.g., fresh-frozen or formalin-fixed paraffin-embedded (FFPE) nucleic acid specimen. It is also envisioned that a sample is from a single individual, a collection of nucleic acid samples from genetically related members, multiple nucleic acid samples from genetically unrelated members, multiple nucleic acid samples (matched) from a single individual such as a tumor sample and normal tissue sample, or genetic material from a single source that contains two distinct forms of genetic material such as maternal and fetal DNA obtained from a maternal subject, or the presence of contaminating bacteria DNA in a sample that contains plant or animal DNA. In some embodiments, a source of nucleic acid material includes nucleic acids obtained from a newborn (e.g., a blood sample for newborn screening). In some embodiments, provided methods comprise amplification of multiple target-specific sequences from a single nucleic acid sample. In some embodiments, provided methods comprise target-specific amplification of two or more target sequences from two or more nucleic acid samples or species. In certain embodiments, provided methods comprise amplification of highly multiplexed target nucleic acid sequences from a single sample. In particular embodiments, provided methods comprise amplification of highly multiplexed target nucleic acid sequences from more than one sample, each from the same source organism.

[0099] In some embodiments a sample comprises a mixture of target nucleic acids and non-target nucleic acids. In certain embodiments a sample comprises a plurality of initial polynucleotides which comprises a mixture of one or more target nucleic acids and may include one or more non-target nucleic acids. In some embodiments a sample comprising a plurality of polynucleotides comprises a portion or aliquot of an originating sample; in some embodiments, a sample comprises a plurality of polynucleotides which is the entire originating sample. In some embodiments a sample comprises a plurality of initial polynucleotides is isolated from the same source or from the same subject at different time points.

[0100] In some embodiments, a nucleic acid sample includes cell-free nucleic acids from a biological fluid, nucleic acids from a tissue, nucleic acids from a biopsied tissue, nucleic acids from a needle biopsy, nucleic acids from a single cell or nucleic acids from two or more cells. In certain embodiments, a single reaction mixture contains 1-100 ng of the plurality of initial polynucleotides. In some embodiments a plurality of initial polynucleotides comprises a formalin fixed paraffin-embedded (FFPE) sample; genomic DNA; RNA; cell free DNA or RNA; circulating tumor DNA or RNA; fresh frozen sample, or a mixture of two or more of the foregoing; and in some embodiments a the plurality of initial polynucleotides comprises a nucleic acid reference standard. In some embodiments, a sample includes nucleic acid molecules obtained from biopsies, tumors, scrapings, swabs, blood, mucus, urine, plasma, semen, hair, laser capture micro-dissections, surgical resections, and other clinical or laboratory obtained sample. In some embodiments, a sample is an epidemiological, agricultural, forensic or pathogenic sample. In certain embodiments, a sample includes a reference. In some embodiments a sample is a normal tissue or well documented tumor sample. In certain embodiments a reference is a standard nucleic acid sequence (e.g., Hg19).

Target Nucleic Acid Sequence Analysis

[0101] Provided methods and compositions of the invention are particularly suitable for amplifying, optionally tagging, and preparing target sequences for subsequent analysis. Thus, in some embodiments, methods provided herein include analyzing resulting library preparations. For example, methods comprise analysis of a polynucleotide sequence of a target nucleic acid, and, where applicable, analysis of any tag sequence(s) added to a target nucleic acid. In some embodiments wherein multiple target nucleic acid regions are amplified, provided methods include determining polynucleotide sequences of multiple target nucleic acids. Provided methods further optionally include using a second tag sequence(s), e.g., barcode sequence, to identify the source of the target sequence (or to provide other information about the sample source). In certain embodiments, use of prepared library composition is provided for analysis of the sequences of the nucleic acid library.

[0102] In particular embodiments, use of prepared tagged library compositions is provided for further analyzing the sequences of the target nucleic acid library. In some embodiments determination of sequences comprises determining the abundance of at least one of the target sequences in the sample. In some embodiments determination of a low frequency allele in a sample is comprised in determination of sequences of a nucleic acid library. In certain embodiments, determination of the presence of a mutant target nucleic acid in the plurality of polynucleotides is comprised in determination of sequences of a nucleic acid library. In some embodiments, determination of the presence of a mutant target nucleic acid comprises detecting the abundance level of at least one mutant target nucleic acid in the plurality of polynucleotides. For example, such determination comprises detecting at least one mutant target nucleic acid is present at 0.05% to 1% of the original plurality of polynucleotides in the sample, detecting at least one mutant target nucleic acid is present at about 1% to about 5% of the polynucleotides in the sample, and/or detecting at least 85%-100% of target nucleic acids in sample. In some embodiments, determination of the presence of a mutant target nucleic acid comprises detecting and identification of copy number variation and/or genetic fusion sequences in a sample.

[0103] In some embodiments, nucleic acid sequencing of the amplified target sequences produced by the teachings of this disclosure include de novo sequencing or targeted re-sequencing. In some embodiments, nucleic acid sequencing further includes comparing the nucleic acid sequencing results of the amplified target sequences against a reference nucleic acid sequence. In some embodiments, nucleic acid sequencing of the target library sequences further includes determining the presence or absence of a mutation within a nucleic acid sequence. In some embodiments, nucleic acid sequencing includes the identification of genetic markers associated with disease (e.g., cancer and/or inherited disease).

[0104] In some embodiments, prepared library of target sequences of the disclosed methods is used in various downstream analysis or assays with, or without, further purification or manipulation. In some embodiments analysis comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In certain embodiments analysis is carried out by high throughput next generation sequencing. In particular embodiments sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon.

[0105] In some embodiments, library prepared according to the methods provided herein is then further manipulated for additional analysis. For example, \ prepared library sequences is used in downstream enrichment techniques known in the art, such a bridge amplification or emPCR to generate a template library that is then used in next generation sequencing. In some embodiments, the target nucleic acid library is used in an enrichment application and a sequencing application. For example, sequence determination of a provided target nucleic acid library is accomplished using any suitable DNA sequencing platform. In some embodiments, the library sequences of the disclosed methods or subsequently prepared template libraries is used for single nucleotide polymorphism (SNP) analysis, genotyping or epigenetic analysis, copy number variation analysis, gene expression analysis, analysis of gene mutations including but not limited to detection, prognosis and/or diagnosis, detection and analysis of rare or low frequency allele mutations, nucleic acid sequencing including but not limited to de novo sequencing, targeted resequencing and synthetic assembly analysis. In one embodiment, prepared library sequences are used to detect mutations at less than 5% allele frequency. In some embodiments, the methods disclosed herein is used to detect mutations in a population of nucleic acids at less than 4%, 3%, 2% or at about 1% allele frequency. In another embodiment, libraries prepared as described herein are sequenced to detect and/or identify germline or somatic mutations from a population of nucleic acid molecules. In certain embodiments, sequencing adaptors are ligated to the ends of the prepared libraries generate a plurality of libraries suitable for nucleic acid sequencing.

[0106] In some embodiments, methods for preparing a target-specific amplicon library are provided for use in a variety of downstream processes or assays such as nucleic acid sequencing or clonal amplification. In some embodiments, the library is amplified using bridge amplification or emPCR to generate a plurality of clonal templates suitable for nucleic acid sequencing. For example, optionally following target-specific amplification a secondary and/or tertiary amplification process including, but not limited to, a library amplification step and/or a clonal amplification step is performed. "Clonal amplification" refers to the generation of many copies of an individual molecule. Various methods known in the art is used for clonal amplification. For example, emulsion PCR is one method, and involves isolating individual DNA molecules along with primer-coated beads in aqueous bubbles within an oil phase. A polymerase chain reaction (PCR) then coats each bead with clonal copies of the isolated library molecule and these beads are subsequently immobilized for later sequencing. Emulsion PCR is used in the methods published by Marguilis et al. and Shendure and Porreca et al. (also known as "polony sequencing", commercialized by Agencourt and recently acquired by Applied Biosystems). Margulies, et al. (2005) Nature 437: 376-380; Shendure et al., Science 309 (5741): 1728-1732. Another method for clonal amplification is "bridge PCR," where fragments are amplified upon primers attached to a solid surface. These methods, as well as other methods of clonal amplification, both produce many physically isolated locations that each contain many copies derived from a single molecule polynucleotide fragment. Thus, in some embodiments, the one or more target specific amplicons are amplified using for example, bridge amplification or emPCR to generate a plurality of clonal templates suitable for nucleic acid sequencing.

[0107] In some embodiments, at least one of the library sequences to be clonally amplified are attached to a support or particle. A support can be comprised of any suitable material and have any suitable shape, including, for example, planar, spheroid or particulate. In some embodiments, the support is a scaffolded polymer particle as described in U.S. Published App. No. 20100304982, hereby incorporated by reference in its entirety. In certain embodiments methods comprise depositing at least a portion of an enriched population of library sequences onto a support (e.g., a sequencing support), wherein the support comprises an array of sequencing reaction sites. In some embodiments, an enriched population of library sequences are attached to the sequencing reaction sites on the support, wherein the support comprises an array of 10² - 10¹⁰ sequencing reaction sites.

[0108] Sequence determination means determination of information relating to the sequence of a nucleic acid and may include identification or determination of partial as well as full sequence information of the nucleic acid. Sequence information may be determined with varying degrees of statistical reliability or confidence. In some embodiments sequence analysis includes high throughput, low depth detection such as by qPCR, rtPCR, and/or array hybridization detection methodologies known in the art. In some embodiments, sequencing analysis includes the determination of the in depth sequence assessment, such as by Sanger sequencing or other high throughput next generation sequencing methods. Next-generation sequencing means sequence determination using methods that determine many (typically thousands to billions) nucleic acid sequences in an intrinsically massively parallel manner, e.g. where many sequences are read out, e.g., in parallel, or alternatively using an ultra-high throughput serial process that itself may be parallelized. Thus, in certain embodiments, methods of the invention include sequencing analysis comprising massively parallel sequencing. Such methods include but are not limited to pyrosequencing (for example, as commercialized by 454 Life Sciences, Inc., Branford, Conn.); sequencing by ligation (for example, as commercialized in the SOLiD^™. technology, Life Technologies, Inc., Carlsbad, Calif.); sequencing by synthesis using modified nucleotides (such as commercialized in TruSeq ^™ and HiSeg^™. technology by Illumina, Inc., San Diego, Calif.; HeliScope ^™ by Helicos Biosciences Corporation, Cambridge, Mass.; and PacBio Sequel@ or RS systems by Pacific Biosciences of California, Inc., Menlo Park, Calif.), sequencing by ion detection technologies (e.g., Ion Torrent ^™ technology, Life Technologies, Carlsbad, Calif.); sequencing of DNA nanoballs (Complete Genomics, Inc., Mountain View, Calif.); nanopore-based sequencing technologies (for example, as developed by Oxford Nanopore Technologies, LTD, Oxford, UK), and like highly parallelized sequencing methods.

[0109] For example, in certain embodiments, libraries produced by the teachings of the present disclosure are sufficient in yield to be used in a variety of downstream applications including the Ion Xpress^™ Template Kit using an Ion Torrent^™ PGM system (e.g., PCR-mediated addition of the nucleic acid fragment library onto Ion Sphere^™ Particles)(Life Technologies, Part No. 4467389) or Ion Torrent Proton^™ system). For example, instructions to prepare a template library from the amplicon library can be found in the Ion Xpress Template Kit User Guide (Life Technologies, Part No. 4465884), hereby incorporated by reference in its entirety. Instructions for loading the subsequent template library onto the Ion Torrent^™ Chip for nucleic acid sequencing are described in the Ion Sequencing User Guide (Part No. 4467391), hereby incorporated by reference in its entirety. Similarly, sequencing using other platforms (e.g., PacBio, Illumina, Helicos, Complete Genomics, Oxford Nanopore) may be carried out using adapted methodologies to incorporate the relevant template preparation according to the instructions and guidance provided with each of the respective platforms.

[0110] The initiation point for the sequencing reaction may be provided by annealing a sequencing primer to a product of a solid-phase amplification reaction. In this regard, one or both of the adaptors added during formation of template library may include a nucleotide sequence which permits annealing of a sequencing primer to amplified products derived by whole genome or solid-phase amplification of the template library. Depending on implementation of an embodiment of the invention, a tag sequence and/or target nucleic acid sequence may be determined in a single read from a single sequencing primer, or in multiple reads from two different sequencing primers. In the case of two reads from two sequencing primers, a 'tag read' and a "target sequence read' are performed in either order, with a suitable denaturing step to remove an annealed primer after the first sequencing read is completed.

[0111] In some embodiments, a sequencer is coupled to server that applies parameters or software to determine the sequence of the amplified target nucleic acid molecules. In certain embodiments, the sequencer is coupled to a server that applies parameters or software to determine the presence of a low frequency mutation allele present in a sample.

EMBODIMENTS

[0112] In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Optionally one or more tag sequences are comprised in each of the plurality of adaptors. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences.. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

[0113] In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and a tag sequence is included in at least one adaptor, and the cleavable moieties are included flanking either end of the tag sequence, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences.. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

[0114] In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety and the melting temperature of each universal sequence is higher than the melting temperature of each target nucleic acid sequence and each tag sequence present. Optionally one or more tag sequences are comprised in each of the plurality of adaptors. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences.. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

[0115] In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Optionally one or more tag sequences are comprised in each of the plurality of adaptors. Such methods are carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences.. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

[0116] In one embodiment, a method for preparing a library of target nucleic acid sequences is provided comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and amplifying the repaired target amplicons in a second amplification using universal primers, wherein each of the plurality of adaptors comprise a universal handle sequence and a target nucleic acid sequence and a cleavable moiety and all of the adaptors comprise tag sequences having cleavable groups flanking either end of the tag sequence, wherein at least two and up to one hundred thousand target specific adaptor pairs are included, and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety and the universal handle sequence does not include the cleavable moiety. Such methods thereby produce a library of target nucleic acid sequence. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences.. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

[0117] In one embodiment, provided is a method for preparing a library of target nucleic acid sequences comprising contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences in the sample under conditions wherein the target nucleic acid(s) undergo a first amplification, digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons, and amplifying the repaired target amplicons in a second amplification using universal primers; wherein each of the plurality of adaptors comprises a universal handle sequence, one or more tag sequences, a target nucleic acid sequence and a cleavable moiety; and wherein at least two and up to one hundred thousand target specific adaptor pairs are included and wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included in the flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety. In certain embodiments the melting temperature of each universal sequence is higher than the melting temperature of each target nucleic acid sequence and each tag sequence present. Such methods thereby produce a library of target nucleic acid sequence. In particular embodiments such methods are carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries. In some embodiments, the digestion and repair is carried out in a single step. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted with the digestion and repair reagents simultaneously. In other embodiments the digestion and repair step is carried out in a temporally separate manner at different temperatures. In particular embodiments the plurality of gapped polynucleotide products in digestion are contacted sequentially with the digestion and repair reagents. In some embodiments one or more of the method steps is conducted in manual mode or in an automated mode or a combination thereof. In particular embodiments each of the method steps is carried out in automated mode. In some embodiments the foregoing methods further comprise at least one purification step. In particular embodiments a purification step is carried out only after the second universal amplification step. In other particular embodiments a purification is carried out after the digestion and repair step and an additional purification is carried out after the second universal amplification. In some of the embodiments adaptor-dimer by products resulting from the first amplification are removed from the resulting library, and in some embodiments an enriched population of amplified target nucleic acids contains a reduced amount of adaptor-dimer byproduct. In certain embodiments, adaptor-dimer byproducts are eliminated. In the foregoing methods the plurality of adaptors capable of amplification of two or more target nucleic acid sequences comprises a multiplex of adaptor pairs capable of amplification of target nucleic acid sequences. In certain embodiments all of the adaptors comprise tag sequences having cleavable groups flanking either end of the tag sequences. In some embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences. In certain embodiments each generated target specific amplicon sequence includes at least 1 different sequence and up to 10⁷ different sequences. In some embodiments, the foregoing methods further comprise analyzing the sequence of the resulting library of target nucleic acid sequences. Such analyzing comprises sequencing by traditional sequencing reactions, high throughput next generation sequencing, targeted multiplex array sequence detection, or any combination of two or more of the foregoing. In other embodiments, the foregoing methods further comprise determining the abundance of at least one of the target nucleic acid sequences in the sample. Such determining is carried out by high throughput throughput next generation sequencing in certain embodiments. In particular embodiments, such sequencing is carried out in a bidirectional manner, thereby generating sequence reads in both forward and reverse strands for any given amplicon. In some embodiments the foregoing methods comprise digestion reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. apurinic endonuclease (e.g., APE1), RecJf, formamidopyrimidine [fapy]-DNA glycosylase (fpg), Nth endonuclease III, endonuclease VIII, polynucleotide kinase (PNK), Taq DNA polymerase, DNA polymerase I and/or human DNA polymerase beta. In some embodiments, the foregoing methods methods comprise repair reagent selected from any one or a combination of Phusion DNA polymerase, Phusion U DNA polymerase, SuperFi DNA polymerase, Taq DNA polymerase, Human DNA polymerase beta, T4 DNA polymerase and/or T7 DNA polymerase, SuperFiU DNA polymerase, E. coli DNA ligase, T3 DNA ligase, T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, and/or 9°N DNA ligase. In particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG), apurinic endonuclease (e.g., APE1), Taq DNA polymerase, Phusion U DNA polymerase, SuperFiU DNA polymerase, 7 DNA ligase. In more particular embodiments the foregoing methods comprise digestion and repair reagent selected from any one or a combination of uracil DNA glycosylase (UDG),. formamidopyrimidine [fapy]-DNA glycosylase (fpg), Phusion U DNA polymerase, Taq DNA polymerase, SuperFiU DNA polymerase, T4 PNK and T7 DNA ligase. In preferred embodiments, the foregoing methods generate compositions comprising nucleic acid library. In particularly preferred embodiments, generated compositions comprising nucleic acid library are useful for analysis of sequences. In specific embodiments, use comprises determination of low frequency allele(s) in a sample.

[0118] In one embodiment provided is a composition comprising a plurality of nucleic acid adaptors, wherein each of the plurality of adaptors comprise a 5' universal handle sequence, one or more tag sequences, and a 3' target nucleic acid sequence wherein each adaptor comprises a cleavable moiety, the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety, and at least two and up to one hundred thousand target specific adaptor pairs are included. In some embodiments the melting temperature of each adaptor universal sequence is higher than the melting temperature of each target nucleic acid sequence and each tag sequence present in the same adaptor. The provided compositions allow for rapid production of highly multiplexed targeted libraries. In particular embodiments, the composition comprises multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences. In certain embodiments, each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences In certain embodiments, compositions each generated target specific amplicon produced by target specific pairs of the plurality of adaptors produces at least 1 different sequence and up to 10⁷ different sequences. The foregoing compositions comprise adaptors wherein they are single stranded or double stranded. Yet additional embodiments provide kits comprising the adaptor compositions of any of the foregoing embodiments. In some embodiments such kits further comprise any one or more of an amplification reagent, a digestion reagent and a repair reagent. In certain embodiments such kits further comprise an amplification reagent, a digestion reagent and a repair reagent.

EXEMPLIFICATION

Example 1

[0119] Provided methods of the invention comprise streamlined procedures enabling rapid, highly multiplexed PCR. See FIG. 1. The invention optionally allows for the incorporation of one or more unique tag sequences, if so desired. Exemplary methods of the invention comprise the following protocols:

Example 1A

Materials and Method

[0120] Optional Reverse Transcription (RT) Reaction method (lOuL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

[0121] 2uL 5x SuperScript^™ VILO^™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤ 8uL volume of DNA+RNA sample for ≤ 20ng total amount of DNA+RNA sample (∼1% RNA sample of the total nucleic acid (TNA));
nuclease-free H2O to the above tube/well to make lOuL total reaction volume;

Method:

[0122] 

42C for 30 min

85C for 1 min

4C hold (indefinitely)

Amplification:

Materials

[0123] 

ul	dH2O (to 30ul final)
ul	20 ng genomic DNA sample
48 nM	Panel of Adaptors
15ul	PhusionU multiplex PCR master mix
2.4ul	2u/ul Phusion U DNA polymerase

Amplification:

[0124] 

98C for 2min

3 cycles of the following:

98C for 30s

64C for 2min

62C for 2min

60C for 4min

58C for 2min

72C for 30s

72C for 2min

4C hold (indefinitely).

Digestion, Fill-in, Ligation:

Materials

[0125] 

2ul	(5u/ul) UDG,
4ul	(10u/ul) FPG
0.5ul	(10u/ul) T4 PNK
1ul	(3000u/ul) T7 ligase
1ul	(lOmM) ATP.

Method

[0126] Mix the materials above, add to reaction mixture.

[0127] Incubate:

30C for 20min

55C for 20min

25C for 10min

98C for 2min

4C hold (indefinitely)

[0128] The resulting repaired sample is purified using 35ul Ampure^® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

Amplification:

Materials

[0129] 1ul for each P1 and A-universal primers, optionally containing barcode sequence (Ion Xpress^™ Adapters, Thermo Fisher Scientific)

Method

[0130] Incubate:
98C for 2min

[0131] 22 cycles of

98C for 15s

64C for 15s

72C for 15s

[0132] 72C for 5min

[0133] 4C hold (indefinitely)

[0134] The resulting sample is purified using 35ul Ampure^® beads (Beckman Coulter, Inc.) according to the manufacturer instructions. Optionally, the purification step is repeated 1X to 2X.

Example 1B

Materials and Method

[0135] Optional Reverse Transcription (RT) Reaction method (lOuL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

[0136] 2uL 5x SuperScript^™ VILO^™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤ 8uL volume of DNA+RNA sample for ≤ 20ng total amount of DNA+RNA sample (∼1% RNA sample of the total nucleic acid (TNA));
nuclease-free H2O to the above tube/well to make lOuL total reaction volume;

Method:

[0137] 

42C for 30 min

85C for 1 min

4C hold (indefinitely)

Amplification:

Materials

[0138] 

ul	dH2O (to 30ul final)
ul	20 ng genomic DNA sample
48 nM	Panel of Adaptors
15ul	PhusionU multiplex PCR master mix
2.4ul	2u/ul Phusion U DNA polymerase

Amplification:

[0139] 

98C for 2min

3 cycles of the following:

98C for 30s

64C for 2min

62C for 2min

60C for 4min

58C for 2min

72C for 30s

72C for 2min

4C hold (indefinitely).

Digestion, Fill-in, Ligation:

Materials

[0140] 

2ul	(5u/ul) UDG,
4ul	(10u/ul) APE1
0.5ul	(lu/ul) Taq polymerase
1ul	(3000u/ul) T7 ligase
1ul	(lOmM) ATP.

Method

[0141] Mix the materials above, add to reaction mixture.

[0142] Incubate:

30C for 20min

55C for 20min

25C for 10min

98C for 2min

4C hold (indefinitely)

Amplification:

Materials

[0143] 1ul for each P1 and A-universal primers, optionally containing barcode sequence (Ion Xpress^™ Adapters, Thermo Fisher Scientific)

Method

[0144] Incubate:
98C for 2min

[0145] 22 cycles of

98C for 15s

64C for 15s

72C for 15s

[0146] 72C for 5min
4C hold (indefinitely)

[0147] The resulting sample is purified using 35ul Ampure^® beads (Beckman Coulter, Inc.) according to the manufacturer instructions. Optionally, purification step may be repeated 1X to 2X.

Example 1C

Materials and Method

[0148] Optional Reverse Transcription (RT) Reaction method (lOuL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

[0149] 2uL 5x SuperScript^™ VILO^™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤ 8uL volume of DNA+RNA sample for ≤ 20ng total amount of DNA+RNA sample (∼1% RNA sample of the total nucleic acid (TNA));
nuclease-free H2O to the above tube/well to make lOuL total reaction volume;

Method:

[0150] 

42C for 30 min

85C for 1 min

4C hold (indefinitely)

Amplification:

Materials

[0151] 

_ul	dH2O (to 30ul final)
_ul	Genomic DNA sample (∼20ng)
6ul	Adaptor Panel 250nM
15ul	PhusionU multiplex PCR master mix (F-562)
3.0ul	2u/ul SuperFiU DNA Polymerase

Amplification

[0152] Assemble mixture of materials in reaction in 96-well plate wells, amplify using method:

99C for 2min

3 cycles of the following:

99C for 30s

64C for 2min

62C for 2min

60C for 4min

58C for 2min

72C for 30s

72C for 2min

4C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

[0153] 

O.lul	VIP Oligo 10 uM (P/N 4385451Thermo Fisher Scientific, Inc.)
2ul	(5u/ul) UDG
4ul	(10u/ul) APE1 (NEB, M0282L)
0.5ul	(lu/ul) Taq polymerase (EP0404)
1ul	(3000u/ul) T7 ligase (NEB M0318L)
1ul	(lOmM) ATP

Method

[0154] Mix the above materials, add into reaction mixture
Incubate:

30C for 15min

50C for 15min

55C for 15min

25C for 10min

98C for 2min

4C hold (indefinitely)

Amplification

Materials

[0155] 1ul for each P1 and A-Barcode-universal primers optionally containing barcode sequence (Ion Xpress^™ Adapters, Thermo Fisher Scientific)

Method

[0156] Add into the reaction wells the above materials, amplify:

99C for 2min

20 cycles:

99C for 20s

64C for 20s

72C for 20s

72C for 5min

4C hold (indefinitely)

[0157] The resulting sample is purified using 1X Ampure^® beads (Beckman Coulter, Inc.) according to the manufacturer instructions. Optionally, purification step may be repeated 1X to 2X.

Example 1D

Materials and Method

Optional Reverse Transcription (RT) Reaction method (lOuL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

[0158] 2uL 5x SuperScript^™ VILO^™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤ 8uL volume of DNA+RNA sample for ≤ 20ng total amount of DNA+RNA sample (∼1% RNA sample of the total nucleic acid (TNA));
nuclease-free H2O to the above tube/well to make lOuL total reaction volume;

Method:

[0159] 

42C for 30 min

85C for 1 min

4C hold (indefinitely)

Amplification:

[0160] 

Materials

_x_ul	nuclease free dH2O (x to 30ul final)
_y_ul	Genomic DNA sample (y ∼20ng) or y lOuL of RT reaction for DNA+RNA sample
12.5ul	Adaptor Panel for ∼50nM each primer concentration
7.5ul	Platinum™ SuperFi™ PCR master mix , replacing SuperFi enzyme with 0.96 U/ µL SuperFiU™ DNA Polymerase
3.0ul	2U/ul SuperFiU™ DNA Polymerase

optionally, an control may be included in reaction, (e.g, Acrometrix Oncology Hotspot Control (Thermo Fisher Scientific))

Amplification

[0161] Assemble mixture of materials in reaction in 96-well plate wells, seal, vortex and centrifuge plate, amplify using method:

99C for 1 s
3 cycles of the following:

99C for 30s

64C for 2min

60C for 6min

72C for 30s

then 72C for 2min

4C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

[0162] 

O.lul	VIP Oligo 0.2 uM (P/N 4385451Thermo Fisher Scientific, Inc.)
2ul	(5u/ul) UDG
4ul	(8U/ul) APE1 (NEB, M0282L)
0.5ul	(0.1 U/ul) Taq polymerase (EP0404)
1ul	(6000U/ul) T7 ligase (NEB M0318L)
1ul	(2mM) ATP
0.5ul	mAB2A7 (0.6mg/mL)
0.25ul	mAB5D3 (0.25mg/mL)

Method

[0163] Mix the above materials, add into reaction mixture, seal plate, vortex and centrifuge Incubate:

30C for 15min

50C for 15min

55C for 15min

25C for 10min

98C for 2min

4C hold (indefinitely)

Amplification

Materials

[0164] 1ul for each P1 and A-Barcode-universal primers optionally barcoded sequence (Ion Xpress^™ Adapters, Thermo Fisher Scientific); or 1uL each of lOuM BC1-Ah, and 1uL of lOuM P1-P1h (IonCode^™ Barcode Adapters, Thermo Fisher Scientific), for uni-directional library

Method

[0165] Add into the reaction wells the above materials, seal plate, vortex and centrifuge, then amplify:

99C for 15s

5 cycles:

99C for 15s

62C for 20s

72C for 20s

15 cycles:

99C for 15s

70C for 40s

72C for 5min

4C hold (indefinitely)

[0166] The resulting sample is purified using 1X Ampure^® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

[0167] Optionally, purification may be repeated 1X to 2X.

Example 1E

Materials and Method

Amplification:

[0168] 

Materials

x_ul	dH2O (x to 30ul final)
y_ul	Genomic DNA sample (y∼20ng) or y lOuL of RT reaction for DNA+RNA sample
12.5ul	Adaptor Panel for ∼50nM each primer concentration
7.5ul	Platinum™ SuperFi™ PCR master mix , replacing SuperFi enzyme with 0.96 U/ µL SuperFiU™ DNA Polymerase
3.0ul	2u/ul SuperFiU™ DNA Polymerase

Amplification

[0169] Assemble mixture of materials in reaction in 96-well plate wells, seal plate, vortex and centrifuge, then amplify using method:

99C for 1 s
3 cycles of the following:

99C for 30s

64C for 2min

60C for 6min

72C for 30s

72C for 2min

4C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

[0170] 

0.1ul	VIP Oligo 0.2 uM (P/N 4385451Thermo Fisher Scientific, Inc.)
2ul	(5u/ul) UDG
4ul	(8U/ul) APE1 (NEB, M0282L)
0.5ul	(0.1 U/ul) Taq polymerase (EP0404)
1ul	(6000U/ul) T7 ligase (NEB M0318L)
1ul	(2mM) ATP
0.5ul	mAB2A7 (0.6mg/mL)
0.25ul	mAB5D3 (0.25mg/mL)

Method

[0171] Mix the above materials, add into reaction mixture, seal plate, vortex and centrifuge Incubate:

30C for 15min

50C for 15min

55C for 15min

25C for 10min

98C for 2min

4C hold (indefinitely)

Amplification

Materials

[0172] 1uL of lOuM BC1-Ah, 1uL of lOuM P1-Uh, 1.5uL of lOuM BC1-Uh, and 1.5uL of lOuM P1-Ah. herein for bi-directional library preparation. BC1-Ah comprises barcode sequence and complementary sequence to universal A handle of forward adapters herein; BC1-Uh comprises barcode sequence and complementary sequence to universal handle of any of reverse adapters B, C, D, or E herein; P1-Uh comprises Ion adapter P1 adapter sequence, barcode sequence, and complementary sequence to universal B, C, D, or E handle of any of reverse adapters B, C, D, or E herein; P1-Ah comprises Ion adapter P1 adapter sequence, barcode sequence, and complementary sequence to universal handle of A handle of forward adapters herein. See FIG. 7.

Method

[0173] Add into the reaction wells the above materials, seal plate, vortex, centrifuge then amplify:

99C for 15s

5 cycles:

99C for 15s

62C for 20s

72C for 20s

15 cycles:

99C for 15s

70C for 40s

72C for 5min

4C hold (indefinitely)

The resulting sample is purified using 1X Ampure^® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

[0174] Optionally, purification may be repeated 1X to 2X.

Example 1F

Materials and Method

Optional Reverse Transcription (RT) Reaction method (lOuL reaction) may be carried out in samples where RNA and DNA are analyzed:

Materials

[0175] 2uL 5x SuperScript^™ VILO^™ (Thermo Fisher Scientific) mix into a microtube or microwell, ≤ 8uL volume of DNA+RNA sample for ≤ 20ng total amount of DNA+RNA sample (∼1% RNA sample of the total nucleic acid (TNA));
nuclease-free H2O to the above tube/well to make lOuL total reaction volume;

Method:

[0176] 

42C for 30 min

85C for 1 min

4C hold (indefinitely)

Amplification:

[0177] 

Materials

_x_ul	nuclease free dH2O (x to 30ul final)
_y_ul	Genomic DNA sample (y ∼20ng) or y lOuL of RT reaction for DNA+RNA sample
12.5ul	Adaptor Panel for ∼50nM each primer concentration
7.5ul	Platinum™ SuperFi™ PCR master mix , replacing SuperFi enzyme with 0.96 U/ µL SuperFiU™ DNA Polymerase
3.0ul	2U/ul SuperFiU™ DNA Polymerase

optionally, a control may be included in reaction, (e.g, Acrometrix Oncology Hotspot Control (Thermo Fisher Scientific))

Amplification

[0178] Assemble mixture of materials in reaction in 96-well plate wells, seal, vortex and centrifuge plate, amplify using method:

99C for 1 s 3 cycles of the following:

99C for 30s

64C for 2min

60C for 6min

72C for 30s

then 72C for 2min

4C hold (indefinitely)

Digestion, Fill-in, Ligation:

Materials

[0179] 

0.1ul	VIP Oligo 0.2 uM (P/N 4385451Thermo Fisher Scientific, Inc.)
2ul	(5u/ul) UDG
4ul	(8U/ul) APE1 (NEB, M0282L)
0.5ul	(0.1 U/ul) Taq polymerase (EP0404)
1ul	(6000U/ul) T7 ligase (NEB M0318L)
1ul	(2mM) ATP
0.5ul	mAB2A7 (0.6mg/mL)
0.25ul	mAB5D3 (0.25mg/mL)

Method

[0180] Mix the above materials, add into reaction mixture, seal plate, vortex and centrifuge Incubate:

30C for 15min

50C for 15min

55C for 15min

25C for 10min

98C for 2min

4C hold (indefinitely)

Amplification

Materials

[0181] 1ul for each of (1) P5-index-A-handle primer; (2) P5-index-I-handle primer; (3) P7-index-A-handle primer; and (4) P7-index-I-handle primer . See Table F.

Method

[0182] Add into the reaction wells the above materials, seal plate, vortex and centrifuge, then amplify:

99C for 15s

5 cycles:

99C for 15s

62C for 20s

72C for 20s

15 cycles:

99C for 15s

70C for 40s

72C for 5min

4C hold (indefinitely)

[0183] The resulting sample is purified using 1X Ampure^® beads (Beckman Coulter, Inc.) according to the manufacturer instructions.

[0184] Optionally, purification may be repeated 1X to 2X.

Example 2

[0185] The first step of provided methods comprises a few rounds of amplification, for example, three to six cycles of amplification, and in certain instances, three cycles of amplification using forward and reverse adaptors to each gene specific target sequence. Each adaptor contains a 5'universal sequence, and a 3' gene specific target sequence. In some embodiments adaptors optionally comprise a unique tag sequence located between the 5' universal and the 3' gene specific target sequences.

[0186] In specific embodiments wherein unique tag sequences are utilized, each gene specific target adaptor pair includes a multitude of different unique tag sequences in each adaptor. For example, each gene specific target adaptor comprises up to 4096 TAGs. Thus, each target specific adaptor pair comprises at least four and up to 16,777,216 possible combinations.

[0187] Each of the provided adaptors comprises a cleavable uracil in place of thymine at specific locations in the forward and reverse adaptor sequences. Positions of uracils (Us) are consistent for all forward and reverse adaptors having unique tag sequences, wherein uracils (Us) are present flanking the 5' and 3' ends of the unique tag sequence when present; and Us are present in each of the gene specific target sequence regions, though locations for each gene specific target sequence will inevitably vary. Uracils flanking each unique tag sequence (UT) and in gene-specific sequence regions are designed in conjunction with sequences and calculated Tm of such sequences, to promote fragment dissociation at a temperature lower than melting temperature of the universal handle sequences, which are designed to remain hybridized at a selected temperature. Variations in Us in the flanking sequences of the UT region are possible, however designs keep the melting temperature below that of the universal handle sequences on each of the forward and reverse adaptors. Exemplary adaptor sequence structures comprise:

Forward Adaptor:

Rev Adaptor B

Rev Adaptor C

Rev Adaptor D

Rev Adaptor E

[0188] Wherein each N is a base selected from A, C, G, or T and the constant sections of the UT region are used as anchor sequences to ensure correct identification of variable (N) portion. The constant and variable regions of the UT can be significantly modified (e.g., alternative constant sequence, >3Ns per section) as long as the Tm of the UT region remains below that of the universal handle regions. Importantly, cleavable uracils are absent from each forward (e.g., TCTGTACGGTGACAAGGCG (SEQ ID NO:6) and reverse (e.g., CTCTATGGGCAGTCGGTGAT(SEQ ID NO:7) universal handle sequence.

[0189] Enzymes used for amplification include (but are not limited to): Phusion U DNA polymerase; SuperFi U DNA polymerase; Taq DNA polymerase; Veraseq Ultra DNA polymerase. SuperFi U DNA Polymerase is a modified version of high fidelity SuperFi DNA Polymerase, available from Thermo Fisher Scientific. SuperFiU DNA comprises a modification in the uracil-binding pocket (e.g., AA 36) and a family B polymerase catalytic domain (e.g., AA 762). SuperFiU is described in US Provisional patent application no 62/524,730 filed June 26, 2017, and International Patent application no. PCT/EP2018/066896, filed June 25, 2018 which are each hereby incorporated by reference. Polymerase enzymes may be limited in their ability to utilize uracil and/or any alternative cleavable residues (e.g., inosine, etc.) included into adaptor sequences. In certain embodiments, it may also be advantageous to use a mixture of polymerases to reduce enzyme specific PCR errors.

[0190] The second step of methods involves partial digestion of resulting amplicons, as well as any unused uracil-containing adaptors. For example, where uracil is incorporated as a cleavable site, digestion and repair includes enzymatic cleavage of the uridine monophosphate from resulting primers, primer dimers and amplicons, and melting DNA fragments, then repairing gapped amplicons by polymerase fill-in and ligation. This step reduces and potentially eliminates primer-dimer products that occur in multiplex PCR. In some instances, digestion and repair are carried out in a single step. In certain instances, it may be desirable to separate digestion and repair- steps temporally. For example, thermolabile polymerase inhibitors may be utilized in conjunction with methods, such that digestion occurs at lower temperatures (25-40°C), then repair is activated by increasing temperature enough to disrupt a polymerase-inhibitor interaction (e.g., polymerase-Ab), though not high enough to melt the universal handle sequences.

[0191] Uracil-DNA Glycosylase (UDG) enzyme can be used to remove uracils, leaving abasic sites which can be acted upon by several enzymes or enzyme combinations including (but not limited to) : APE 1-Apurinic/apyrimidinic endonuclease; FPG-Formamidopyrimidine [fapy]-DNA glycosylase; Nth-Endonuclease III; Endo VIII-Endonuclease VIII; PNK-Polynucleotide Kinase; Taq- Thermus aquaticus DNA polymerase; DNA pol I-DNA polymerase I; Pol beta-Human DNA polymerase beta. In a particular implementation, the method uses Human apurinic/apyrimidinic endonuclease, APE1. APE1 activity leaves a 3'-OH and a 5'deoxyribose-phosphate (5'-dRP). Removal of the 5'-dRP can be accomplished by a number of enzymes including recJ, Polymerase beta, Taq, DNA pol I, or any DNA polymerase with 5'-3' exonuclease activity. Removal of the 5'-dRP by any of these enzymes creates a ligatable 5'-phosphate end. In another implementations, UDG activity removes the Uracil and leaves and abasic site which is removed by FPG, leaving a 3' and 5'-phosphate. The 3'-phosphate is then removed by T4 PNK, leaving a polymerase extendable 3'-OH. The 5'-deoxyribose phosphate can then be removed by Polymerase beta, fpg, Nth, Endo VIII, Taq, DNA pol I, or any other DNA polymerase with 5'-3' exonuclease activity. In a particular implementation Taq DNA polymerase is utilized.

[0192] Repair fill-in process can be accomplished by almost any polymerase, possibly the amplification polymerase used for amplification in step 1 or by any polymerase added in step 2 including (but not limited to) : Phusion DNA polymerase; Phusion U DNA polymerase; SuperFi DNA polymerase; SuperFi U DNA polymerase; TAQ; Pol beta; T4 DNA polymerase; and T7 DNA polymerase. Ligation repair of amplicons can be performed by many ligases including (but not limited to) : T4 DNA ligase; T7 DNA ligase; Taq DNA ligase. In a particular implementation of the methods, Taq DNA polymerase is utilized and ligation repaired in accomplished by T7 DNA ligase.

[0193] A last step of library preparation involves amplification of the repaired amplicons by standard PCR protocols using universal primers that contain sequences complementary to the universal handle sequences on the 5' and 3' ends of prepared amplicons. For example, an A-universal primer, and a P1 universal primer, each part of the Ion Express Adaptor Kit (Thermo Fisher Scientific, Inc.) may optionally contain a sample specific barcode. The last library amplification step may be performed by many polymerases including, but not limited to : Phusion DNA polymerase; Phusion U DNA polymerase; SuperFi DNA polymerase; SuperFi U DNA polymerase; Taq DNA polymerase; Veraseq Ultra DNA polymerase.

[0194] 2A, In one specific implementation, adaptors were designed using the composition design approach provided herein, including universal handle-unique tag-gene specific target sequence described in Example 2 above, and targeted to genes using the ONCOMINE^™ Focus Research Panel (Thermo Fisher Scientific, Inc.) target sequences and ION AMPLISEQ^™ Designer (Thermo Fisher Scientific, Inc). Forward and reverse adaptors described above were utilized comprising

Forward Adaptor:

Rev Adaptor B

[0195] With target sequences specific to targets as in Table A, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Preparation of library was carried out according to the method described above for Example 1A. Formamidopyrimidine [fapy]-DNA glycosylase (FPG) /UDG enzyme is utilized for digestion, which is expected to create abasic sites at all uracil positions, FPG is expected to cleave on the 5' and 3' side of the abasic site (leaving a 3'-phosphate and a 5' phosphate) and removal of the 3'phosphate (by T4 PNK for example) should produce an extendable 3'-OH and a ligatable 5'-phosphate. However, as shown by the BioAnalyzer trace (See FIGURE 2), this process consistently failed to generate recoverable product. The process can be rescued however by the addition of an additional purification step post-repair. The purification process can be anything inactivates and removes the repair enzymes prior to the next amplification step. Similar results were obtained if endoVIII was utilized.

[0196] 2B. In another specific implementation, adaptors were prepared as described in section 2A for targets of the ONCOMINE^™ Focus Assay. See Table B. Forward and reverse adaptors described above were utilized comprising

Forward Adaptor:

Reverse Adaptor was any of Rev Adaptor B, Rev Adaptor C, Rev Adaptor D, Rev Adaptor E: Rev Adaptor B

Rev Adaptor C

Rev Adaptor D

Rev Adaptor E

[0197] With target sequences specific to targets as in Table B, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Preparation of library was carried out according to the method described above for 1C. See FIGURE 3, Table 1. Similar successful sequencing results were generated with each of the reverse adaptor pairings.

Example 3

[0198] Prepared libraries are sequenced, and analyzed. Sequencing can be carried out by a variety of known methods, including, but not limited to sequencing by synthesis, sequencing by ligation, and/or sequencing by hybridization. Sequencing has been carried out in the examples herein using the Ion Torrent platform (Thermo Fisher Scientific, Inc.), however, libraries can be prepared and adapted for analysis, e.g., sequencing, using any other platforms, e.g., Illumina, PacBio, etc. Result may be analyzed using a number of metrics to assess performance, for example:

o # of families (with ng input DNA captured) The median # of families is a measure of the number of families that maps to an individual target. In this case, each unique molecular tag is a family.

∘ Uniformity is a measure of the percentage of target bases covered by at least 0.2x the average read depth. This metric is used to ensure that the technology does not selectively under-amplify certain targets.

∘ Positives/Negatives: When a control sample with known mutations is utilized is analyzed (e.g., Acrometrix Oncology Hotspot Control DNA, Thermo Fisher Scientific, Inc.), the number of True Positives can be tracked.

▪ True Positives: The number of True Positives informs on the number of mutations that were present and correctly identified.

▪ False positives(FP): (Hot spot and Whole Target) The number of False Positives informs on the number of mutations that are determined to be present, but known not to be in the sample.

▪ False negatives (FN) (if acrometrix spike-in is used) The number of False Negatives informs on the number of mutations that were present but not identified.

∘ On/Off Target is the percentage of mapped reads that were aligned/not aligned over a target region. This metric is used to ensure the technology amplifies predominantly the targets to which the panel was designed.

∘ Low quality is tracked to ensure the data is worth analyzing. This metric is a general system metric and isn't directly related to this technology.

Example 4

[0199] One benefit of the instant invention is the ability to use Ampliseq.com designer in conjunction with the provided methodology. Adaptors were designed using the composition design approach provided herein, including universal handle-unique tag-gene specific target sequence described in Example 2 above, and targeted to genes using the ONCOMINE^™ Focus Research Panel (Thermo Fisher Scientific, Inc.) target sequences and ION AMPLISEQ^™ Designer (Thermo Fisher Scientific, Inc). Forward and reverse adaptors described above were utilized comprising

Forward Adaptor:

Rev Adaptor B

[0200] With target sequences specific to targets as in Table A, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Library was prepared using 20ng of genomic DNA and ∼1% Acrometrix Oncomine^™ Hotspot Control (AOHC) DNA (Thermo Fisher Scientific, Inc.), according to the protocol described above in Example 1C. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). Performance with the panel (eg., yield, uniformity) indicates the technology is able to effectively make use of the designer pipeline. See Figure 4A-4C.

[0201] Results using the AOHC DNA (shown in Table 1) demonstrate that, using this protocol, we effectively identify most of the True Positives (71 or 75) present in the AOHC and importantly did not generate any False positives.

TABLE 1

	Oncology Panel (Ex 4)	BRCA Panel (Ex 5)	Oncology HotSpot Panel (Ex 3)	Oncology HotSpot Bidirectional (ex 6)
True Positives	75	NA	NA	NA
TP in SNP, INDEL	71;4	NA	NA	NA
False Negatives	3	NA	NA	NA
False Positives	0	0	0	0
Uniformity	98.60%	100%	100%	100%
Low Quality	15%	28%	31%	26%
On Target	98%	95%	96%	95%
# of Families	4398	5208	8755	6391

Example 5

[0202] Adaptors were designed according to the composition design approach provided herein, including universal handle-unique tag-gene specific target sequence described in Example 2 above, and targeted to genes using the BRCA Research Panel (Thermo FisherScientific, Inc.) target sequences and ION AMPLISEQ^™ Designer (Thermo Fisher Scientific, Inc). Forward and reverse adaptors described above were utilized comprising

Forward Adaptor:

Rev Adaptor B

[0203] With target sequences specific to targets as in Table C, and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Library was prepared using 20ng genomic DNA according to the protocol described above in Example 1C Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.).. Similar to Example 5, performance (e.g., yield, uniformity) with the panel indicates the technology is able to use the designer pipeline. See Figure 5 and Table 1.

Example 6

[0204] Primers were designed using the composition design approach provided herein and targeted to oncology genes using those of the panel target sequences as described above in Example 4, except that the library amplification step utilized two primer pairs (to put the two universal sequences on each end of amplicons, e.g., an A-universal handle and a P1-universal handle on each end) to enable bi-directional sequencing. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). See Figure 7. Performance (e.g., yield, uniformity) with the instant panel indicates the technology is able to use the designer pipeline and effectively generate sequencing data for both strands of DNA. See Figure 6A-6C and Table 1.

Example 7

[0205] Primers were designed using the composition design approach provided herein and targeted to a wide variety of oncology target sequences. Forward and reverse adaptors described above were utilized comprising

Forward Adaptor:

[0206] 

[0207] Rev Adaptor C

TABLE 2A: Family Generation, Coverage, and Uniformity

Sample	Input	AmpliSeq HD
		Median Read Counts per Target	Uniformity (U50)	Median # Families Size>=3	Molecular Conversion	Median # Families Size>=3
cfDNA 2016B	20 ng	61, 939	95.9%	5794	48%	5794
		63,679	95.9%	5879	49%	5879
cfDNA 416G	20 ng	79,004	98.6%	7676	64%	7676
		61.694	98.6%	7322	61%	7322
0.5% fMM	6000 copies	61.458	98.6%	5466	46%	5466
		62.019	98.6%	5685	47%	5685
0.1% fMM	6000 copies	70.397	98.6%	6278	52%	6278
		60,879	98.6%	5946	50%	5946
gDNA	292 copies	22.650	97.3%	340	57%	340
		79.746	98.6%	354	59%	354

TABLE 2B: Sensitivity, Specificity, and FPs/lib, Hot Spots Only

Sample	Input	AmpliSeq HD
		Sensitivity (%)	Specificity (%)	FP
cfDNA 2016B	20 ng		100.00	0
		99.70	99.70	1
cfDNA 416G	20 ng		100.00	0
		100.00	100.00	0
0.5% allelic Frequency	6000 copies	100.0	100.00	0
		100.0	100.00	0
0.1% allelic Frequency	6000 copies	85.14	100.00	0
		94.60	100.00	0
gDNA	292 copies		100.00	0
			100.00	0

[0208] With target sequences specific to targets as in Table D and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Samples containing 19.8ng of cell free DNA and 0.2 ng of total RNA were processed as described in example 1D, starting with the optional reverse transcriptase step. Total RNA for some samples listed contained 5 spiked in fusion constructs. See Table D. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). Performance (e.g., yield, uniformity, molecular conversion, sensitivity) with the instant panel indicates the technology can efficiently convert input DNA into library and detect mutations present at frequencies as low as 0.1% to 0.5%. See Table 2A-2B. Additionally, results confirm the technology can efficiently convert input DNA and cDNA into library and detect fusions present at frequencies of -1%. See Table 3A-3B.

TABLE 3A Fusions

LRIG3-ROS1	EZR-ROS1	KLC1-ALK
CCDC6-RET	GOPC-ROS1	SDC4-ROS1
CD74-ROS1	HIP1-ALK	SLC34A2-ROS1
CUX1-RET	KIF5B-ALK	TPM3-ROS1
EML4-ALK	KIF5B-RET	TPR-ALK

TABLE 3B: Family Generation, Coverage, and Uniformity (No Activation)

Sample	Input	FP	U50	Conversion
cfDNA 5022	10 ng	0(343)	98.5	44%
		0 (323)
cfDNA 5022 +total RNA	10 ng	0(343)	99.25	51%
		2 (323)
cfDNA 5022 +Trifusion	10 ng	0(343)	98.5	50%
		1 (323)
gDNA	10 ng	0(343)	93.98	45%
		2 (323)
gDNA +total RNA	10 ng	0(343)	93.98	54%
		0(323)
gDNA +Trifusion	10 ng	1 (343)	95.49	53%
		1 (323)

Example 8

[0209] Primers were designed using the composition design approach provided herein and targeted to genes using those of short tandem repeats (STRs), which are useful for high resolution genotyping and analysis of complex mixtures. Forward and reverse adaptors described above were utilized comprising
Forward Adaptor:

Rev Adaptor E

[0210] With target sequences specific to targets as in Table E and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair. Samples containing 1 to 10 ng of genomic DNA were processed as described in example 1D without the optional reverse transcriptase step. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.). Performance (e.g., yield, uniformity) with the instant panel indicates that even challenging STR targets (which are often shortened by 1 or more repeats during amplification) can be efficiently converted into a library. Results were consistent across titration levels of input DNA. See Table 4. When results were compared to standard operating procedure according to manufacturer instructions using Torrent Suite Molecular Diagnostics plugin to evaluate the same targets, results generated using compositions and methods provided herein yielded more consistent signal over each of the repeat regions, with less stutter (data not shown).

TABLE 4:

Barcode Name	Input DNA	Median Read Counts per Target	Median # Families Size>=3	Half-Double Uniformity (Families Size>=3)	80% Uniformity (Families Size>=3)
BC_0102	1ng	37,727	257	77.78%	63.89%
BC_0105	2ng	35,056	412	83.33%	63.89%
BC_0108	5ng	32,478	1021	80.56%	69.44%
BC_0120	10ng	30,915	1646	86.11%	63.89%

Example 9

[0211] Primers were designed using the composition design approach provided herein and targeted to oncology genes target sequences as described above in Example 6, where two primer pairs were utilized in library amplification (to put the two universal sequences on each end of amplicons, e.g., an A-universal handle and a P1-universal handle on each end) to enable bi-directional sequencing. Library preparation was carried out on samples containing spiked in AOHC control as described according to methods of Example 1E above without optional RT step. See Figure 7. Prepared library was sequenced using Ion 520/530 Templating/Sequencing kits and instrumentation (Thermo Fisher Scientific, Inc.), then analyzed separately for unidirectional sequence results as well as results analyzed from bidirectional sequencing. Performance (e.g., yield, uniformity, sensitivity) with the instant panel indicates the technology is able to use the designer pipeline and effectively generate sequencing data for both strands of DNA, and bidirectional sequence analysis results in reduction of indel False Positives measured. See Table 5.

TABLE 5

	Bidirectional, Analyzed Unidirectional	Bidirectional, Analyzed Bidirectional
True Positives	67	67
Sensitivity	91.8	91.8
TP in SNP, INDEL	65;2	65;2
False Negatives	6	6
False Positives in SNP, INDEL	1:2	1:0

Example 10

[0212] For each of the Ion barcode adaptors, a single barcode is included in an A adapter. Addition of a second set of barcodes on the P1 adapter can effectively reduce the level of contamination artifacts in results by filtering out identified contamination reads. Primers were designed using the composition design approach provided herein and targeted to a wide variety of oncology target sequences. Samples containing 20ng of genomic DNA were processed similarly to those described in Example 7 above and using the method of example 1D, however, additionally barcoded P1 adapters were also utilized, wherein a barcode 12mer sequence was inserted into the P1 adapter sequence of the reverse adapator. Sample containing genomic DNA for library preparation was processed with barcode 8 in both A and P1 adapters. Additional samples were also processed with barcodes 1,2 ,3, 4, 5, 6, 7 and 9 (each in both P1 and A barcoded adapters), but without genomic DNA. Performance (e.g., yield, uniformity, Conversion) with the instant panel indicates that additional barcodes can effectively identify contamination. See Table 6.

TABLE 6:

Reverse Barcode	Reads Detected	% Total
bc1	332	0.001%
bc2	54	0.000%
bc3	261	0.001%
bc4	481	0.001%
bc5	9,908	0.019%
bc6	8,532	0.016%
bc7	2,656	0.005%
bc8	52,089,480	99.941%
bc9	1,403	0.003%
bc10	7,131	0.014%

Example 11

[0213] In another specific implementation, adaptors were prepared as described in example 2A for targets of the ONCOMINE^™ Focus Assay, as in Table B, as well as described in example 6 with target sequences specific to targets as in Table D and adaptors each comprise 4096 unique tag sequences for each gene specific target sequence, resulting in an estimate of 16,777,216 different unique tag combinations for each gene specific target sequence pair.. Forward and reverse adaptors utilized comprising
Forward Adaptor:

Rev Adaptor I:

[0214] Preparation of library was carried out according to the method described above for 1F. See also FIGURE 8. The workflow has been adapted to use amplification primers to enable libraries to carry out sequencing runs on the Illumina platform. The design (shown schematically in Figure 8) contains: (1) P5 grafting primer region; (2) P5 index(A-H) region; (3) P5 sequencing/index read primer region; (4) A-handle region; (5) UT region; (6) gene specific insert; (7) UT region; (8) I-handle region; (9) P7 sequencing/index read primer region; (10) P7 index (1-12) region; and (11) P7 grafting primer region. 3 libraries were made with an oncology panel comprising targets of Table D having idex5-01-idex7-5, idex5-02-index7-6 and idex5-7-idex7-7 respectively. 2 libraries were made with Focus panel comprising targets of Table B having idex5-01-idex7-5, and idex5-7-idex7-7 respectively. See Table F. All libraries are made with 19.6ng of g24385 with 0.4ng spike-in AOHC so we could detect 0.1% allele frequency.

TABLE F

Name	Sequence (5' to 3')	SEQ ID
5-01-Ah		1706
5-02-Ah		1707
5-07-Ah		1708
5-08-Ah		1709
5-09-Ah		1710
5-010-Ah		1711
5-013-Ah		1712
5-014-Ah		1713
01-Ih		1714
02-lh		1715
5-07-Ih		1716
5-08-Ih		1717
5-09-Ih		1718
5-010-Ih		1719
5-013-lh		1720
5-014-lh		1721
7-1-Ah		1722
7-2-Ah		1723
7-3-Ah		1724
7-4-Ah		1725
7-5-Ah		1726
7-6-Ah		1727
7-7-Ah		1728
7-8-Ah		1729
7-9-Ah		1730
7-10-Ah		1731
7-1-Ah		1732
7-12-Ah		1733
7-1-lh		1734
7-2-Ih		1735
7-3-lh		1736
7-4-lh		1737
7-5-Ih		1738
7-6-lh		1739
7-7-Ih		1740
7-8-lh		1741
7-9-Ih		1742
7-10-Ih		1743
7-11-Ih		1744
7-12-Ih		1745

[0215] To mimic low level of mutant variants (0.1%) presence in DNA samples, we used purified genomic DNA and spiked in small quantity of AcroMetrix Oncology Hotpot Control plasmid. These samples are used as our control samples for the purpose of demonstrating the library preparation method and assessing the sensitivity and specificity for low levels mutant variants detection by this assay method. Bioanalyzer results matched library structure designs, and yield and purity of libraries were on par with those prepared on other methods described above. Similar successful sequencing results were generated with each of the adaptor pairings.

[0216] A MiSeq sequencing run successfully generated clusters, and produced sequencing and indexing reads. Sequencing results of the panel run on the Illumina MiSeq indicate similar performance as compared to the standard AmpliSeq HD version run on the Ion S5 using a 540 chip. See Table 7.

TABLE 7

	MiSeq	S5540
Raw Read Accuracy (%)	99.31	99.27
Mapped Reads	12,994,280	17,855,575
Mean Depth	46,674	62,429
On-Target (%)	98.91	98.64
coverageAnalysis Uniformity (%)	97.86	97.98
Half-Double Uniformity (%)	86.62	83.64
0.1% MegaMix TP	140	138
0.1% MegaMix FN	11	13
0.1% MegaMix FP	58	38

[0217] While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

TABLE A

Primer Name	SEQ ID	Primer Sequence (target of primer A)	Primer Name	SEQ ID	Primer Sequence (target seq of primer B)
F1	8	GCTCCCAGGCACUTGATGAUAC	R1	104	ACAGAAUCACAUGCCACACAGT
F2	9	TGTTGCCATTUCAGGGTTTCUGA	R2	105	TTCCTTCUAAAAGGCCATGAAGATCUG
F3	10	ACCAAUGCGAGGAAGAAAAACAAUC	R3	106	TCTGAAGAACAUGTGUGAGCACA
F4	11	TCTTCAGAAU CTTGTTGGCU GCAT	R4	107	CCCAACCCACAUTTCCTTTATAGATGTUT
F5	12	AGAGTTGCAUCCTTCCCTTCUCT	R5	108	TGTTCCAACAGGAUCTGUCCAAAA
F6	13	CTGGCAUGACGCAGTTTCTUC	R6	109	CCAGTGTCTGUCCTTGCCTTUC
F7	14	GATCAAAGAGACGAAGUCTCTUGCA	R7	110	CUATGACAAGAAAAUGGACACCAACAAG
F8	15	CTTGCCUAGACAGCACCGUAAT	R8	111	AGGAGGAUAAAGACCTGGUCCAT
F9	16	TGGTTTCTGGUGGGACCATTAUG	R9	112	GTCCTCUGGATCTCTTCAUGCA
F10	17	TTGAAAGAGAACACACUTACTCUCCAC	R10	113	CTGAGACATTCCUATGTCCTGCUC
F11	18	CTCTACCAGAGUTAATCAACTGAUGCA	R11	114	TUGAUACAAAACAAGCCCACGAACT
F12	19	TATCAACTGTCCUTGTTGGCAAAUCA	R12	115	CCAGCCTAATCTUGTTTTTCTTATGTTCUG
F13	20	GCAAATGACTUGCTATTATTGAUGGCA	R13	116	GTTATAGATGGUGAAACCTGTTTGTUGG
F14	21	GTGGGATCATAUTCATCTACAAAGUGGT	R14	117	GATTACTGGTTUCCAACAGGTTCTUG
F15	22	GGAGGTCAUGGCATCGAGUT	R15	118	TATGGTCTUGGACATCCAGGAUCT
F16	23	GTGAGGCAGUCTTTACUCACCT	R16	119	TAGGAAATGCAUTTCCTTTCTUCCCA
F17	24	GGGAAATGUGAGCCCTUGAGAT	R17	120	CCTGTGGCUGTCAGTATTUGGA
F18	25	ACTCTTGCUCCTTCCATCCTUG	R18	121	GTTCATCCUGCTGGAGCUCAT
F19	26	CCCAAUGCAGCGAACAATGTUC	R19	122	GTAGCTGCTGAAAAUGTAACTTTGTAUCC
F20	27	GATCAGGGCUTCCAUGAGGAAA	R20	123	ACTCTGTAGGCUGCAGTTCUCA
F21	28	CTCAAGAGUGAGCCACTTCTUACC	R21	124	CTCCTCTTGUCTTCTCCTTUGCA
F22	29	AGAATAAAACACAUACAAGTTGGAAATTTCUGG	R22	125	CTTGTGAGTGGAUGGGTAAAACCUAT
F23	30	ACCUGAGCCAAGGACTTTUACC	R23	126	CGGACTGAAAGUATAACCTTCTTCTTUCC
F24	31	TGTCAATTAGCUGGAACATCUGAAACT	R24	127	GCATGTGAACAUTCTGCTTTTCAUGG
F25	32	GTGCCCTATUACCTCAATCAUCCT	R25	128	ACGCCTTCACCUTTAACACCUC
F26	33	CCAGACAGAAAAGCGGCUGTUA	R26	129	ACTTGGGAGGUATCCACAUCCT
F27	34	CCTAGTAGAATGTTUACTACCAAATGGAAUGA	R27	130	AGATTCATCTUGAAGAAGTTGAUGGAGG
F28	35	TTTTTGAUGAAACAAGACGACTTTGUG	R28	131	GAATAGGATATTGUATCATACCAATTTCUCGAT
F29	36	CACAGCUACACCATATATGAAUGGAGA	R29	132	CAGCATTTGACTTUACCTTATCAATGTCUC
F30	37	GATCTATGTUCGAACAGGTATCUACCATG	R30	133	ACTGCTAAACACTAAUATAACCTTTGGAAAUAT
F31	38	GGGAAGAAAAGUGTTTTGAAATGTGTUT	R31	134	CATTTTTCCAGATACUAGAGTGTCTGTGUA
F32	39	TTTGAATCTTUGGCCAGTACCUCA	R32	135	CATAAGAGAGAAGGUTTGACTGCCAUAAA
F33	40	GACTAGCUAGAGACAATGAATUAAGGGAAAA	R33	136	GAATCTCCATTTUAGCACTTACCTGUGA
F34	41	CTGAGATGCACAAUAAAACAGTUAGCC	R34	137	AGAATGTCAGTUAAGTTAATGAGCTTTUCCAT
F35	42	GACAUTCUCAAACAGGAGAAGAAGGA	R35	138	GCTTGATUCCAAGGACCATGATCUG
F36	43	TCTTTTCTCAAGUTGGCCTGAAUCA	R36	139	CAATTCCCAAAAUGAAGGTAGCUACAC
F37	44	CAATCTTTTGAUGACATTGCATACATUCGA	R37	140	GGAAGATCCAAUCCATTTTTGTTGUCC
F38	45	GTATGCAGGCAUCCTCAGCUA	R38	141	CGGGAAGCGGGAGAUCTUG
F39	46	CUGGUGACCGAGGACAACGT	R39	142	GGCGTCCUACTGGCAUGA
F40	47	GTCCUGGGAGTCUCAGGACA	R40	143	CCTUCAGCAGCTUGAAGAGCT
F41	48	CCAGTTACCUGTCCTGGTCAUT	R41	144	GGAAACTCCCAUCTTGAGTCAUAAGG
F42	49	AGTGAAAAACAAGCUCTCATGTCUGA	R42	145	CATGTGTCCAGUGAAAATCCUCACT
F43	50	GGAAAAATTGUGAAGATCTGTGACTTUGG	R43	146	CTGACTUTAGAGATTAAAGUGAAGGAGGAT
F44	51	AGCACTCTGACAUATGGCCATUT	R44	147	CCTGGACAAAAAUACCAATCTATTGUGG
F45	52	GGCACGGTUGAATGTAAGGCTUA	R45	148	ACTGATATGGUAGACAGAGCCUAAACAT
F46	53	CCCACAGAAACCCAUGTAUGAAGT	R46	149	ACTGACCAAAACUCAGCCTGUT
F47	54	TUGACAGAACGGGAAGCCCUCAT	R47	150	CCTGACAGACAAUAAAAGGCAGCUT
F48	55	CCTTACTCAUGGTCGGAUCACAA	R48	151	GTTGAAACUAAAAATCCTTUGCAGGACT
F49	56	CCAATATTATGGAUCCCAACTGCCUA	R49	152	ACATTCTGAAGCAGCUTGGAGTUT
F50	57	GCTACTTTGAUTTCTCCACTUCCAAC	R50	153	GAGGAGATTGAAAAUCTTCCTGCCUT
F51	58	AAAGGCAUGGAGCATCTGUACA	R51	154	TTGGTCCGUCTCCUCCACGG
F52	59	GTTATGTCCUCATTGCCCUCAACA	R52	155	CTTCAGTCCGGUTTTATTTGCATCAUAG
F53	60	CGAGGGCAAAUACAGCTTUGGT	R53	156	GACTCTCCAAGAUGGGATACUCCA
F54	61	TGATGGAGAUGTGATAATTUCAGGAAACA	R54	157	CGGTGACTUACTGCAGCTGTUT
F55	62	GAGACATGCAUGAACATTTTTCUCCA	R55	158	TCCAGACCAGGGUGTTGTTTUC
F56	63	GCCTCTUACACCCAGUGGAGAA	R56	159	TGTGCCAGGGACCUTACCTTAUA
F57	64	CCTTCTCUCTCTGTCAUAGGGACT	R57	160	CACAGCAAAGCAGAAACUCACAUC
F58	65	CTCCAGGAAGCCUACGTGAUG	R58	161	TGTGTUCCCGGACATAGUCCA
F59	66	CAGGAACGUACTGGUGAAAACAC	R59	162	GAAAATGCUGGCTGACCUAAAGC
F60	67	GCTTGTAAGUGCCCGAAGTGUA	R60	163	CACAACCCACUGAGGTATATGTATAGGUAT
F61	68	CGCAGTGCUAACCAAGTTCTTUC	R61	164	CCATGGTTAAATAAAAU GCCACTTACTG UT
F62	69	CAGTCAAGGUTGCTGATTTUGGT	R62	165	CTTGGTGGUAAACTTTTGAGTTUGCA
F63	70	CGAATCGCUACCCTGCTGUT	R63	166	CCAAGCCUCATGGUGCCAT
F64	71	TACCGAUACCGUGCGGG	R64	167	TACUGGCAGCAAGUGCCCAG
F65	72	CTGTCCUCCACAGGCATTTTUG	R65	168	CCCTCACUCACAGCACATAGUC
F66	73	CCATCCCUGACTGTGAGAUCAA	R66	169	CCAGGUACGCCTCCAGAUGA
F67	74	TCAGTGGAAAAAUAGCCTCAATTCTUACC	R67	170	CTTCATGAAGACCUCACAGTAAAAAUAGGT
F68	75	TATTATGACTUGTCACAATGUCACCACAT	R68	171	GACTCGAGTGAUGATTGGGAGATUC
F69	76	TTCCUTAGTCTTTCTTUGAAGCAGCA	R69	172	AGATGCTCUGAGAAAGGCATUAGAAAG
F70	77	TCTGACUCCACGAGAACTTGAUCATA	R70	173	TATTGTTAACCUTGCAGAATGGUCGA
F71	78	CAAGGCAUAAAAGCTGGGAAAUAGG	R71	174	CUACCTGCCUACGCAACAAGAT
F72	79	GGCTAUGGCACCUGCAACT	R72	175	GGGACCUCAGATGTGCTGTUG
F73	80	CCACAGAUCCACTGUGCGAC	R73	176	GTGGCTTGUGGGCAAACTUG
F74	81	CCATCCTGACCUGGTATGGUCA	R74	177	CCTGCTUCAGGACGTTGAACUC
F75	82	CAGCTCGTUCATCGGGACUT	R75	178	ACCTGGCUCCTCTTCACGUA
F76	83	CCTCCTTCCUAGAGAGTTAGAGUAACT	R76	179	CACCCACACUTACACATCACTTUG
F77	84	CACTGTGTTACUGCCATCGACTUA	R77	180	TCGAGATTUAGCAGCCAGAAATGTUT
F78	85	GATTCAATCAAACUGCAGAGTATTUGGG	R78	181	TGATCTGGUGTCAGAGAUGGAGAT
F79	86	GGCTTCTTGG UCGTGTTCTUCA	R79	182	CUAGCGCCUGGAAGAGAAAAGGAGAT
F80	87	CCCAGCGUCCTCAAAAGTUACA	R80	183	CCCTCCACAAUCATTCCTGUGT
F81	88	CTCTACGUCTCCUCCGACCA	R81	184	CTTATTTATTGGTCUCTCATTCTCCCAUCC
F82	89	CCTGTACTGGUGGATGTCCUCA	R82	185	GCCTGTUGGACATCCTGGAUAC
F83	90	CGCCAGGCUCACCTCTAUAG	R83	186	AGGAGCGAUGACGGAATAUAAGC
F84	91	TGTCTTTGCUGATGTTTCAAUAAAAGGAA	R84	187	AGTTAAGGACTCUGAAGATGTACCTAUGG
F85	92	CATGTACTGGUCCCTCATUGCA	R85	188	GTAATAATCCAGACUGTGTTTCTCCCUT
F86	93	TACCTCTATTGTUGGATCATATTCGUCCA	R86	189	TATTATAAGGCCU GCTGAAAATGACU GAAT
F87	94	CAGACACTGUACAAGCTCUACGA	R87	190	GAAUAAAGAGGAGCAGGTUGAGGAA
F88	95	CTCTGUCACAGTGGATUCGAGA	R88	191	CAACATGACGAAGAUGGCAAACTUC
F89	96	TCCUTCCATAGUGACCAAGACCA	R89	192	GGGTACAUACAAAGCAGTCTGUGT
F90	97	GGTTCCATUGGTAGCTGGUGAT	R90	193	GCCCATTTTTATCUACTTCCATCTTGUCA
F91	98	TGTAAAGAGACAGCCUTTCCTCUGA	R91	194	AGTTCACAAAUCCATCAATGTTGCUC
F92	99	ACACUCTUGAGGGCCACAAAG	R92	195	TGTGATTGUAGGGTCTCCCTUGAT
F93	100	CCGCTCCUTGTAGCCAAUGA	R93	196	GGGTCUGACGGGTAGAGUGT
F94	101	CCACUTUGGAACAGGACCAAC	R94	197	TCAAAGTCGTCAUCCTTCAGTTCUC
F95	102	CTTTCTTCCACCUTTCTCCAGCUA	R95	198	CATCGCTGUAGAACGCACCAUA
F96	103	TCAAGCCCUCCAACATCCUAGT	R96	199	GGAAACTTCTGTUCATACCGACATGUAG

TABLE B

Primer Name	SEQ ID	Primer Sequence (target seq of Primer A)	Primer Name	SEQ ID	Primer Sequence (target seq of Primer B/C/D/E)
F97	200	GAGGTCGTATUCGTCCACAAAAUGGT	R97	469	GAGGCAGGAGACCCUGUAGGAG
F98	201	GAAACTGCTTAGUAACTAGCAGAAGTGTUC	R98	470	GAGGATAUATGCCAUACCCCAGCAAA
F99	202	GACAAAGTTGUGTGTTGTAAGUGGAACA	R99	471	GACCAAGAAAGGCUTGTGTCTACATTTUT
F100	203	GAGCACCAATCUTTCTTCTGCCTTTUG	R100	472	GACCAAAUCAAGAAACCTGTTUGAGAGAA
F101	204	GAGGGAUCCCAAGGAAGAGAAGUGA	R101	473	GACACTTCCCUTGTGGGAATGUCAA
F102	205	GAGCTACTCTCCUGAACTCTCTCACUC	R102	474	GATGCATCAGAACCCUCCTTGAAUC
F103	206	GACTCCCAGUTGCAACGTUAGGT	R103	475	GAGGUCCACGGAUCCAGAAACAAG
F104	207	GATCACGUGTCCCCCTUCCA	R104	476	GAGGTTCCTCCUCTCCTGGTCUC
F105	208	GAACATTTGGCUGTGACTTCUAAGAAGAAA	R105	477	GAGCTCACTAACUAACGTGAAAGCCTUAC
F106	209	GAGATGAUCCAGATGTUAGGGCAGT	R106	478	GAGGTTTTGCACAAGUTAGGTTTGTTTUG
F107	210	GAGCCCAAATUGATTTCGATGATCTUCA	R107	479	GAACCTTTATATCGTUACTCTGAATCTTATCTUCC
F108	211	GAGCTCAAGAGUGAGCCACTUCT	R108	480	GATGACTCTGTCUCCTCTTGTCTTCUC
F109	212	GAATTAACACACAUCAGTGGAACTTCUGT	R109	481	GAAAACGTTTTUCACCTTAGCATTTUGT
F110	213	GAGCAAUCCAAAAGAAUAGCAGCCAAA	R110	482	GACACCATCUCCATATCATUGAGACCAAAT
F111	214	GACTTTGTGGAAUAGCCCATGAAGAGUA	R111	483	GACGACAGACUACTTTGGTTCTCTTTUGT
F112	215	GAACAGGAAGAGCACAGUCACTTUG	R112	484	GACTCACUGACAAGCTCCUCGT
F113	216	GACCATGCAGAGUGAAAGGATAUCCC	R113	485	GAGCCTTTTCTTUTGCTTCCCTTGUT
F114	217	GATGGAGCCGCUGACACCUA	R114	486	GACAGGACCUGGCCCUGAC
F115	218	GAGGTGUCTAGCCCAUGGGAGAA	R115	487	GACCCAUCACACACCATAACUCCAC
F116	219	GAGTCTGGUCCACATTGCTCUCA	R116	488	GAGCTGUCCCCTCACCATUCAG
F117	220	GAGCAAGAGUACACACTCCTCATTUGG	R117	489	GATCACAACCCACUGAGGTATATGTAUAGG
F118	221	GACTGGTTTCUGGTGGGACCATUA	R118	490	GACAUGCACCGGAAAAGCGAUG
F119	222	GACTCCCAGGCACUTGATGATACUC	R119	491	GACATTTCTAGGUTACAGGCCUGGAT
F120	223	GAGGGCTUGGTAACGTCCUGT	R120	492	GACTCCAUGCCCCTCACUCA
F121	224	GATGTGTCAAGGAGUTCGAAGATUCAC	R121	493	GAATTGAAAATCUTCCTGCCTUCCCT
F122	225	GAGUACAGCCAGTGTGUCCGA	R122	494	GAGCAAAAGTGGUCCTCTCTGAAUCT
F123	226	GACCATCCGGGCUTTACGCAAAUA	R123	495	GAATATCAUCCAGCCTGTGTCTTUCC
F124	227	GACCCCACUGAACCTCTCTTACATUT	R124	496	GAGAGGGAAGGCAGGAUCTCUAAC
F125	228	GACCCUAACAGCCATGCTTTCUC	R125	497	GACCAGGCAAUGGAAAGGGTACAUA
F126	229	GACGGCGAUGCTGAGAACCAAUA	R126	498	GAGAAUAAAGAGGAGCAGGTUGAGGAA
F127	230	GACCGACGUTGACCGCAUC	R127	499	GAGGGCAAAUGAGCCTCUCAGT
F128	231	GAAAATATTUCAGTGTCCGTUCACACACAA	R128	500	GATCCAGATTGAUCTTGGGAGTGUAAAAA
F129	232	GACCACACUGACGTGCCTCUC	R129	501	GAGTCTTTGTGUTCCCGGACAUAGT
F130	233	GAGCGCCACAGAGAAGUTGTUGA	R130	502	GAGGGTCUGACGGGTAGAGUGT
F131	234	GACCACAAAAUGGATCCAGACAACUGT	R131	503	GAGCTTGCTCTGAUAGGAAAATGAGATCUA
F132	235	GAACTGTTTCGTAUTTATAGCTGATTTGAUGGA	R132	504	GACCTCTTCCUCAGGATTGCCTUT
F133	236	GACCTCAUTGCCCUCAACACAGT	R133	505	GATCAGTCCGGTUTTATTTGCATCATAGUT
F134	237	GACACCACGUACCAGATGGAUGT	R134	506	GACCCAAAGACUCTCCAAGATGGGAUA
F135	238	GAAGACATGCAUGAACATTTTTCUCCAC	R135	507	GATCCAGACCAGGGUGTTGTTTUC
F136	239	GATGUGGAGCCTCTUACACCCA	R136	508	GAGTGCCAGGGACCUTACCTTAUAC
F137	240	GAACGTCTTCCUTCTCTCTCTGUCA	R137	509	GACTGAGGUTCAGAGCCAUGGA
F138	241	GAGAATGTGAAAAUTCCAGTGGCCAUC	R138	510	GAGUCATATCUCCCCAAACCCCAAT
F139	242	GAGGGTGTGUGGTCTCCCAUAC	R139	511	GAGCCATAGGGCAUAAGCTGTGUC
F140	243	GAGGATGAGCUACCTGGAGGAUGT	R140	512	GACCTTGGTCCUTCACCTAACCTUG
F141	244	GAGGTCACTGUACACCTTACACAUGAA	R141	513	GACCCTCUTTAGCCAUGGCAAGG
F142	245	GACATCACUGTAAACCTUGCAGACAAAC	R142	514	GATGGTCTCUCATTCTCCCAUCCC
F143	246	GAGCTTCTTGGUCGTGTTCTTCAUT	R143	515	GACTCCTCCUGTGATCTGCAAUCT
F144	247	GAUGGAAGCCCAGCCATTUCTAAA	R144	516	GAGATGAUGAAGATGATUGGGAAACACAAG
F145	248	GAGCCCCUGAGCGTCAUCT	R145	517	GAGGGCTGUGCGTCACTGUA
F146	249	GAGAGCTGGUGGAGGCUGA	R146	518	GAGGAGCCCAGGCCUTTCUT
F147	250	GAGUGACCGAGGACAACGUGAT	R147	519	GAGCGTCCUACTGGCAUGACC
F148	251	GACTCUGGGAGATCTUCACGCT	R148	520	GACCACUCACAGGTCGTGUGT
F149	252	GAGGATTGCAGAUTGGGCCTUG	R149	521	GAACATGATGGAUGTCACGTTCUCAAA
F150	253	GAATAATCCAUTGCCTGTCUAAAGAACACT	R150	522	GATGTTAACCUTGCAGAATGGUCGAT
F151	254	GAGACTTGGUGTTGTTGAUGGCAAA	R151	523	GACUGCAGGATTCCUACCGGAA
F152	255	GACCAACAUGACTTACTTGAUCCCCAT	R152	524	GAATCACCAAAUGGCACCAUACGA
F153	256	GAACCCUGGCCTACCTGGUC	R153	525	GAAGTTCAAGCUGAAGAAGATGUGGAA
F154	257	GATGAAGCAGCAAGUATGAUGAGCAA	R154	526	GACTGACACCUAGCTGTGATCCUG
F155	258	GAGGCACGGTUGAATGTAAGGCTUA	R155	527	GAACTGATATGGUAGACAGAGCCUAAACAT
F156	259	GACCACACCCUGTTCACTCCTUT	R156	528	GAGTCTCAGTCAUTAGAGCACTCUGG
F157	260	GAAAGGTGATCUATTTTTCCCTTTCUCC	R157	529	GATTTCATACUGACCAAAACUCAGCCT
F158	261	GAGCTTTTTGCUAAAATGCATGTTUCCAA	R158	530	GAGACACGGCUTTACCTCCAAUG
F159	262	GACAAAGAATGGUCCTGCACCAGTAAUAT	R159	531	GAAGGCCTGCUGAAAATGACTGAATAUAA
F160	263	GATCCTCATGUACTGGTCCCTCAUT	R160	532	GAGTAAAAGGUGCACTGTAATAAUCCAGACT
F161	264	GACAGATCTGTATUTATTTCAGTGTTACTUACCT	R161	533	GAGACTCTGAAGAUGTACCTATGGTCCUA
F162	265	GACATGTCAACAUCGCTCTAATUCAGAGA	R162	534	GAGCTTTUCAAAAGGCTUAAACACAGGAT
F163	266	GATGTTACGCAGUGCTAACCAAGUT	R163	535	GAGCAAACCACAAAAGUATACTCCAUGGT
F164	267	GAGCTGAUTTTGGTCTUGCCAGAG	R164	536	GATCTGACTTGGUGGTAAACTTTTGAGUT
F165	268	GACCTCACCTCUATGGTGGGATCAUAT	R165	537	GAGTTCTTGCUGGTGTGAAATGACUG
F166	269	GATTCGCCTGUCCTCATGTATUGG	R166	538	GACACCCCCAGGAUTCTUACAGAAAA
F167	270	GAGCACUGGGACTTTGGTAATUCAC	R167	539	GACATCTCTUGGAAACTCCCATCTUGA
F168	271	GACAGTGAAAAACAAGCUCTCATGTCUG	R168	540	GACCACATGUGTCCAGTGAAAAUCCT
F169	272	GACAGTGTGUCCACCGTGAUCT	R169	541	GAAGTGAAGGAGGAUGAGCCUGA
F170	273	GATGGAATGCCAGAACUACAATCTTTUGAT	R170	542	GAGTGGAAGATCCAAUCCATTTTTGTTGUC
F171	274	GAGACGCAUTTCCACAGCUACAC	R171	543	GAAGCATCAGCAUTTGACTTTACCTTAUCA
F172	275	GAGCTTTGAAUCTTTGGCCAGUACCT	R172	544	GACATAAGAGAGAAGGUTTGACTGCCAUA
F173	276	GAGATGCAGCCAUTGACCTGTTUAC	R173	545	GAAGAAAACCATUACTTGTCCATCGUCT
F174	277	GAGGGATUAAAGCTGGCTAUGGCA	R174	546	GACCTTGTUGGGACCTCAGAUGT
F175	278	GAAGCAUACGCAGCCTGUACC	R175	547	GAGTGGUAGCAGTGGAUGCAGAA
F176	279	GAGCTUCCAGGAGCGATCGTUT	R176	548	GAAGGCCCCAUACAATTTGAUGACA
F177	280	GAAGCTCGTUCATCGGGACTUG	R177	549	GACCATGGUGCACCUGGGAT
F178	281	GACTGGTUACTGAAAGCUCAGGGAT	R178	550	GAACTTTGCGUGGTGTAGATATGAUCAA
F179	282	GAGGACTCTGUGAGTGGGATTTGTTUT	R179	551	GAGTCTTCACUCACCTCGGAUGA
F180	283	GACATCCCUGACTGTGAGAUCAAGAA	R180	552	GACAGGUACGCCTCCAGAUGAG
F181	284	GAATCAACCUGCTTGGTGTCUG	R181	553	GAAACUCCCGCAGGTTUCCCT
F182	285	GAACGAGGACCUGTGGGACUC	R182	554	GAGTGCCTUGCCCTTTTTGUGG
F183	286	GACATUCCCCAACAGCTGUGGT	R183	555	GACCGGGAUGCCAGGAUACG
F184	287	GACCTTCCUCCTGAAGGCCUGA	R184	556	GAGGGCUGTACCTCCUCAGAGA
F185	288	GAAAGTGCUTGTGCCCUGCAT	R185	557	GAACAGGCUGCCCAAGGGCUA
F186	289	GACCCCTCTUGGACCTTAGAUGC	R186	558	GACAGUGATCAGAUGAGCAGCAG
F187	290	GACGCAUGGAGAAGAAACTGCAUG	R187	559	GAACGGUCTUGGAACCCAGAGA
F188	291	GATCCCCTAUGTGCAAGTCCUAAAG	R188	560	GAGCTATTGAUGTCTGCAGTCUGG
F189	292	GACCACTGUGCAGAAGCTCUCC	R189	561	GATUGACTUGCCGGAAGAGCCT
F190	293	GACGCCGGCCUCGTGAGUC	R190	562	GAAGACCUCCGAGTCACTCCUG
F191	294	GACAAATGCUGAAAGCTGTACCAUACC	R191	563	GAAAAAGACTCGGAUGATGTACCTAUGG
F192	295	GATGAGGCAGUCTTTACTCACCUG	R192	564	GATTCCTTTCTUCCCAGAGACATUGC
F193	296	GAGCAAAGACUGGTTCTCACUCACC	R193	565	GAACATCCCUCTCTGCTCUGCA
F194	297	GACGAUCTGTTCUACACGGAACCC	R194	566	GAGGCTGGTTAUTGAAACCTTGTTTUACAT
F195	298	GACCAGACAAGCCUACAGTAGGAAUC	R195	567	GACTACCCCCGUACCAAGUACAAAC
F196	299	GACTCCACAGACCCUCTCCTUGC	R196	568	GATCGUCGAAGCGGCUGAC
F197	300	GAAGGGTGTCUCTCTGTGGCTTUA	R197	569	GAGACTCTGUAGGCTGCAGTTCUC
F198	301	GAGTTTCUGCAGATTGACTUGCACA	R198	570	GACTTCTTCCUACCTGTTTCCCAUGAC
F199	302	GATCAGGAAACAAAAAUTTGTGCTAUGCAA	R199	571	GAGGACCCAUTAGAACCAACUCCAT
F200	303	GAGCTGGAGGAGCUAGAGCTUGAT	R200	572	GAGGCTTGUGGGAGACCTUGAAC
F201	304	GAGGGCTGUCGTGGTAGACTUAGA	R201	573	GACCTGGTAGTCUCAAGCAGATGTTAAUG
F202	305	GAAAGACTTCUCAAATTGTTGCCATTUCAG	R202	574	GAAACGGACATGAGUTTGTTTTCCTTCUA
F203	306	GACGAGGAAGAAAAACAAUCCCACTUG	R203	575	GACAGCCAACAAGAUTCTGAAGAACAUG
F204	307	GAGAGATCCTTUCGAAGTCATCGTCUT	R204	576	GATCCCTAGGUAGCTAACCCCUAC
F205	308	GAGGGCAAUGTCAATTAGCUGGAAC	R205	577	GAAAAACACGGCAUGTGAACATTCUG
F206	309	GACACTGTGTTACUGCCATCGACTUAC	R206	578	GAGTATTCAUCGAGATTUAGCAGCCAGA
F207	310	GACTTTTACCCUCTTCAGCTCAGTTUCT	R207	579	GAGAGAGAGGACUGACTATCGGACUG
F208	311	GATCTCCTCCAACCUAATAGTGTATUCACA	R208	580	GAGACTGUCAAGCAGAGAATGGGUAC
F209	312	GATTTCGUAAGTGTTACUCAAGAAGCAGAA	R209	581	GAGAATAGGATATTGUATCATACCAATTTCUCGAT
F210	313	GAATGCCCCCAAGAAUCCTAGUAGAA	R210	582	GAACGAAAATGUAAGAAGATTCATCTUGAAGAAG
F211	314	GAAGAGATGATTGUTGAATTTTCCTTTUGGG	R211	583	GAAAAGCCATTTTUCCAGATACTAGAGUGT
F212	315	GACGGAACUCGAATCGCUACCCT	R212	584	GAGGGUCCCCAAGACACCUACG
F213	316	GACTCGATGCUGTTCCCAGGUAC	R213	585	GACCGAGAACUGAGGGTGGUACA
F214	317	GATCATACAGACACUTCATTTGGAGUACC	R214	586	GATACTAGAACUCAAAACACTGGCTGUT
F215	318	GAAAAAATAAAGCTUGGCTTCAAGTTGUCT	R215	587	GAGTAAGTCTTCACUTTCAGATTTTAGTUGGG
F216	319	GAACATTGTGACCUTAATTTTGTGATCTCTUG	R216	588	GATGCTTCCTGGUCTTTAGGATTTCUT
F217	320	GACCCCACTCAUGTTTAGCAGATGUA	R217	589	GATTTTACTTCUGCTTGGTGGCAUG
F218	321	GAGGACAGGUTTTGTTGTUGAGGAAG	R218	590	GATTTTACCCTCAUGGCTTAGTAGCATTATUT
F219	322	GAAGCAAGGTCAUAAATTATTCTCCATATTTUCCA	R219	591	GAAAAAATATUCATCCAGCTUCAGGAAAAGG
F220	323	GATCTTTTTACCTUATAGATGGGAAACAUGAGAG	R220	592	GAATCAGTCUGGTGGATGGGUAACA
F221	324	GAATGTGTCTTTCAUGAGAAAAACAAGATCAUT	R221	593	GACTAATAATGAATAAUTGGGTATGAGGCUACAGT^
F222	325	GATAGTAGCTGAUCCACAGAAGTTCAGUA	R222	594	GATGTGAGAGAGCAAUCAAGGAGUG
F223	326	GAAAGACTCTGAAUACCACCATCAAGAATAAUAAA	R223	595	GAGTCTGAGAGUAGAAGGCAGATTCTGUA
F224	327	GAATCTACAGGCCAAUGGTTCCTUC	R224	596	GAAACTTUGCGGAGATCUGAAAACCA
F225	328	GAGCCAGTAGUCACAAAGATTTCTUACCA	R225	597	GACTCTAAAGAAGGAAGUGAGAACTTCUCC
F226	329	GAAGAAGAUTGGGUGGGCAGAC	R226	598	GACTTTCTTCACUCAAAGTGCCTATTTUGAC
F227	330	GAAACCACTGATACAUTTTTCTACTTTCCUGAA	R227	599	GATTCTTTTGAGAACUGAGTGATTTAUGACCT
F228	331	GAAGACTTCTTUGAGATATTTCCATAGCUCAC	R228	600	GAAGAAGTUAGAAACAGAACTGTATGUAAGCAT
F229	332	GACATTTTTGTTTATGUTATTCTCTCTACCUCAGC	R229	601	GAGCTATACGAACTUAGAAGTGAGAAATAATCUT
F230	333	GAAGTTATAGGTAAUCGATGCATATAGCTCAUCT	R230	602	GATTTCTCCAGGUCCAAAATGAATAACTATTUGA
F231	334	GAAATTGTTTGTAGGGUTGGTTATTAGTGACUAT	R231	603	GAATCCAGGAUAGGAAGCACACAUG
F232	335	GACCACTATGUAAGACAAAGGCUGGT	R232	604	GATTTTATAACTAGATUTTCCTTCTCTCCATUCC
F233	336	GAGTTTCTGUAGCCCATACTTTGGAUGA	R233	605	GAAATTCATACAUTTTTCTCTAACUGCAAACAT
F234	337	GACACTGUGAAGGCCCTTTCTTCUG	R234	606	GAGCAGTTGUGAGATTATCTTTTCAUGGC
F235	338	GAGCATAGGAGATAAUCATAGGAATCCCAAAUT	R235	607	GATGTTTTTCTAAUGTGTTAAAGTTCATUGGAAC
F236	339	GAAGTCACTGGAAUTGTTGGGCUAC	R236	608	GACCATGACTGUCACAGTGACCUT
F237	340	GACTUCCAGGAGCCGUAGAGTTT	R237	609	GATTGUGGCCCAAACAAAGCUC
F238	341	GAACTCTTCCTATTUTTGTAGTGACCTGTUT	R238	610	GAGTGCTTGGAAAUGGAATGGTTTUAGAAT
F239	342	GATTCCTGAUAAAGCACAGCTGTAGUG	R239	611	GACTACTGUAACCAAGAGGTGACTUCAG
F240	343	GATTGTUCAAGCAGCGAGUCC	R240	612	GAAGCCGAUATCCCUGCAGAC
F241	344	GACATGAACUACCTGGACCGCUT	R241	613	GAGTCGGUGTAGAUGCACAGCT
F242	345	GAGGTGCTGUCTGGGAAGAUGT	R242	614	GATGCCCAAGGUACTGCAUGGT
F243	346	GAAAAGAGGCAGUAGCATCTTCUCC	R243	615	GACUCACGCCUAAACCAGAACC
F244	347	GAAATCCTGGAGCUTTGGTGTCTAATUC	R244	616	GATAGCTGGCUCCGCACCUT
F245	348	GATGCAGAAGCGGUTTCTGUG	R245	617	GACTGCUGGGCGCCGUAAC
F246	349	GAGCCTCAGAGAUAAAGGCAAAGATUG	R246	618	GAACCCACACAAGCGAAUCTCUG
F247	350	GAACCATTATTTCTTUGTTTTGTTTTTCCTG UAT	R247	619	GAACTTTGCUGCCTTAATGACATUCC
F248	351	GATACCAACCAAGUTTCATUAACCACAGT	R248	620	GAGGTACCUGAGATGGAGGAGUC
F249	352	GACCATGTTGGUCACTTACTCAAAGATTUT	R249	621	GATTGAGCCACUAAGCAGTAACCATUC
F250	353	GAAATGGGCAAGGUATGGATGUGG	R250	622	GACCCGAAGUTCTTCTGCAGUCC
F251	354	GATGGCGCAUCAGATCCTAGTUT	R251	623	GAGCCGAAACGAUCAAGGUGAGT
F252	355	GATGTAACAACCUAAAGGGAATAGGAAGAAUG	R252	624	GATCAGTAGAAAGAUGGTACCAAAAUGGGT
F253	356	GAGGCACTGGUTCTCATTCCUG	R253	625	GAGACCGAGCUCGGGTGUAT
F254	357	GAATGACTCAAUACCAACCCCUCCA	R254	626	GAGCCTTTGTGGUCATGGGAAAGTAUA
F255	358	GACATAACCATGAUATTAATAGGACTCCUGCT	R255	627	GAATTTGCCTGAAATUACACATAGAACTTTCUG
F256	359	GATGAACGCAAAACCUGTTGAAGTUAAAA	R256	628	GAGGGATGGGUGACTGAGAUGGT
F257	360	GACTTAAAAATGTCAAUATCTGGCCTCAAAUACG	R257	629	GAGTGGACAUGCGAAUGGAGGA
F258	361	GAGGGAAGCAATUTGCTACACTTTAATTUAAAC	R258	630	GATTTACTCTGACAGCUAAATGAACTCAAATGUA
F259	362	GAACAGAAGCUTCTAATCCUCAACGT	R259	631	GAAGGCTCAGAACACUTTACTGAATTTUG
F260	363	GAAGTTGAUGCCAATTCACAAUCACCA	R260	632	GATTACTTAGAAGAAAAUTGCTCCTTGUCAGA
F261	364	GACTGAGGTCTATUCACTTTCTTTTCATCTTUG	R261	633	GAGTGAAGGAAACCAUTCGTGAUAAAGC
F262	365	GACTATTTGTTTCTUCCCCATGGAATTGUC	R262	634	GAGAAAATUGGACCCAGTTCTCUGCT
F263	366	GATAATCTTUGAACTGCCTGUGCACT	R263	635	GAATCTTTCAACUGTAAAATTCACTGUGGGT
F264	367	GAAAGCAAUGGCTTGGGAAGUAAGA	R264	636	GACCATTCTCAUATCCTAGGTCUGCCT
F265	368	GATCTAAAGGTTTTTCUGATTTCCTCATTAGGAUT	R265	637	GAGCACUCCATTTUGGACAGCAA
F266	369	GATCCAGTCATTTUGAGAAAGACAACTUACT	R266	638	GAGTTTATTTTCTGGUTTCAATAGAACAAGTUGA
F267	370	GATTCATTAATATTTUCAGATCACCAGTTGATUG	R267	639	GATTTGAAAGGTAGAUTGCCATAATGTATCATUG
F268	371	GAATTAACTGTACCUCCAACTTTCTTACTATAUGC	R268	640	GAATGTGGAATCTUTGTTTAGTTTTACTCUGGT
F269	372	GATTAAGAAACUAGAAACTGTTTAGACUGCCT	R269	641	GAATGGTTTAGTCUGACACATATTTAACACUT
F270	373	GATGGTTCTGUCGACTAAACUGC	R270	642	GATTTTCAAGTTAUAGAAACATGTCATGTTGUCA
F271	374	GAACGGACACUATGTCCTTAAGCUGA	R271	643	GACTAGACTTUGAGACCTGCTAAATAATUAGATG
F272	375	GATTGGCAUGGCTTCTCUAGCT	R272	644	GACAGGUCCAAGUGAACCAGGGA
F273	376	GACACCTTCUACCGCTCACUGC	R273	645	GAAGGGCACUGACCCTGGUA
F274	377	GAATTGACUCTGAATGUCGGCCAA	R274	646	GATCTGCAGGAGGGUGCTCTUA
F275	378	GACTCTGCCCCUAAGAAACCUGGA	R275	647	GAGGGCAACUACACCTGCATUGT
F276	379	GAATTACTCUAACTTTCGCAUGCACAC	R276	648	GATGCCAAGACAGUGAAGTTCAAAUG
F277	380	GAAGUGGGCAGCAGTTTCUGA	R277	649	GAGACACCACCUACTTCTCCGUCA
F278	381	GAAACCAACTGCUTGTATGCTTTCUGG	R278	650	GAAAGACCAAAAGAGAAUGGAAAGTACUGAC
F279	382	GAGCAGCCUTACCTGGTUGGA	R279	651	GAAGAGUATCCATCUCCAGGAGACG
F280	383	GATTACAGCUCGTTGGUGCAGT	R280	652	GATGTGGCUCTCCGCCCAUT
F281	384	GAATGGAAACCCUGACAGAGTCTTUG	R281	653	GAGCTACACCATUAGCTTCACTGATTUT
F282	385	GATGTTATGAGCUTAGCACCTUGCAG	R282	654	GACTGGATGGUAAGAGGAGTTTCTTCAUC
F283	386	GACCAGTTCUGCAGTTAGAGGTUG	R283	655	GACCTTTCCCCUCCCCTACCUAG
F284	387	GATTTGATTCTTAAUCACCTAAGGAUGGCT	R284	656	GACAAAACAAAGUCAAAGAGAATTATGAAATGUG
F285	388	GAATCCGTACCUTCCACCAATCUG	R285	657	GACAGGGATTTUGGTTACTACTTTGCUAAGA
F286	389	GATATAACAATGAAUGACCAAAAGGAAATUAACAA	R286	658	GATTGTCTTCUGGACACGTTCUGAAA
F287	390	GATAACTTTCCATAUGCAAACCTACTGGCUA	R287	659	GATATTAAGCTTTCUTGGAAAATTCTCTTUCCCT
F288	391	GACCUGGACGTCTUGGAAAAGGG	R288	660	GATTCAGAAGTUAGGAAAGGAGUCCAG
F289	392	GATCTGGGUCAAGGAUGGCACA	R289	661	GACACCUGUCACCCGCACAC
F290	393	GAGCCCACUTCCCATCUGGGT	R290	662	GACAGTCAGUAACGCCAGUGAGT
F291	394	GATCCCCGCUGCTGUGCAAC	R291	663	GAGUCCCGTGGUGCAAAGGC
F292	395	GACCCACATGUCCAGCACCUT	R292	664	GAATGTACACTAGTTUCCGGAATAAACCTTUT
F293	396	GAGCTGGUGAAACAGGTAGUGAGT	R293	665	GACTUGACCCCUGCGAGCCA
F294	397	GACTCCAGGUCCTTGTGUGAGC	R294	666	GACCCACUCAAGCTCAGCTGUAA
F295	398	GACCTCACGAACUGTGCTGAUGG	R295	667	GACTGAGAATGGCUACCTCTCGATAUG
F296	399	GAGGATTCGAGAAGUGACAGGCTAUG	R296	668	GAGGCTGGAGUTGGTGTTATAGTUCAA
F297	400	GAATTGGTAGCUGGTGATGTTCCUC	R297	669	GACTCACACATCUTGAGCCCATTTTTAUC
F298	401	GACAGCTAATUCATCTGGAGAUCAAACCC	R298	670	GACTGAGAGGGUGTCACATACCAUG
F299	402	GATGTCAGTTCCCUCCTTTTCTATTTTCUC	R299	671	GATTCATACCGACAUGTAGGACCTUGT
F300	403	GATGGGCACGGUAATGCUGCT	R300	672	GAACTTCUCACACCGCTGTGUT
F301	404	GACTCUGCGGTGGTUGGCAT	R301	673	GACCTCACCUCCGTTTCCUGCA
F302	405	GACTCCACCUCCAGGAACTTACUC	R302	674	GATCUGGCCCCCTUAGGAGGA
F303	406	GAGGGATCTTGUGAAATGTCATCTGACUC	R303	675	GATCATCCTCUCCCCATAGAAAAGUCC
F304	407	GATCAACCCTGTUTTTCTCCCTCTTATUG	R304	676	GATCTCUGCCATCATTUCCGGAAAG
F305	408	GACTGUACAGCATGAAGUGCAAGAAC	R305	677	GATGCAAGGAAUGCGATGAAGUAGA
F306	409	GACCATTAACAUGGCCTACCAGAGUT	R306	678	GAGTCGCUAACACGTGTGTGTUC
F307	410	GATTGCCUAGACAGCACCGTAAUG	R307	679	GATGGCTAAACTUGACCTTTTTACTCUGC
F308	411	GAGACGCAGUTTCTTCTTCTCAUCG	R308	680	GATTCCTCAGCAUCGACCTUGC
F309	412	GATATCGAGTGTGUGCATATGTGTATGTUG	R309	681	GAAATCTATATACTUCCTTACCTGGGATUGGA
F310	413	GAAGGGAAAAUGACAAAGAACAGCUCA	R310	682	GAACATGCTGAGAUCAGCCAAATUC
F311	414	GAGGCCTGCUTTTGGAGTCCUAT	R311	683	GAGCAGUGAAAAGAGTCUCAAACACAA
F312	415	GAGAAGAGCCUCCACCATCUCCA	R312	684	GACCCACAGGCCUTCTUCGAG
F313	416	GACACACAUGCCATCATTCUAGGAAG	R313	685	GACTGGUATGAGAAACUGCACGAGT
F314	417	GAGAGGTTTUCCAGCACTCTGACAUAT	R314	686	GAAATACCAATCUATTGTGGGCTCUGG
F315	418	GATCTTCTCTGUTTCAGGGCAUGAAC	R315	687	GACCTCCTTCUGCATGGTATTCTTUCT
F316	419	GAAGATTCUGCCGAACCAATGGAUC	R316	688	GAATTAAAGCAGUGCTCATGATUGGG
F317	420	GATATGACTUGTCACAATGUCACCACAT	R317	689	GACGGGACUCGAGTGATGATUGG
F318	421	GAGTGCCCTATUACCTCAATCATCCUG	R318	690	GACTTCACCTTUAACACCTCCAGUCC
F319	422	GATCAGTTACTACCUGAAAATGACACTTUGT	R319	691	GACTCCTCTAGCUATCTTAATGACTUGGAC
F320	423	GATAAAGACCTUCTTCCGTGTGUCCT	R320	692	GACTGCTTTCATUCATAGGGAAATACAUAAGAAA
F321	424	GATACATTTATTTUGAGAAACTTGAGAGAACUTCA	R321	693	GATTCAATATTTTAAAUAGTCTGGCCUAAACGGT
F322	425	GAAGATGGTGATAGAUCTTTAAGAGAATTGCUT	R322	694	GATGATTTCCAGUATTAATTGGCAAUAAGAGAAT
F323	426	GAAGCTTTTGATAAGAGUTAGGAAATCACTAGUC	R323	695	GAATGAAAGCUAAAACATAAGATGAAUGGGAAAA
F324	427	GAAGGAUAAAAACCAGCATTATTTATTUGAGCA	R324	696	GAATTATTTCTTACCACUTTTCCTTTCTCCUGT
F325	428	GACTGACCCAUAATCTTGCACCATTUACC	R325	697	GAATTGTGAGATUAACAGCAGGGAUACC
F326	429	GATTTGAAATGAAUGTTCACGACAAAUGC	R326	698	GAGCTTCATTGTCTUGATAAAATTTATGGTATCUT
F327	430	GAACAACCAAAACAAUACACACAGAGATTUT	R327	699	GACCAGCTCTTUCATATCTTAACATTUAGCAACA
F328	431	GAACGGAGGGUCATGTGTATATTAAGUAAG	R328	700	GAGCCAAAACATTTUGTCCCTTTCTATAATTUG
F329	432	GAGAATTAAGUGTGTACTACUCCCAAGAGAAAA	R329	701	GATGGACTTCAAGUGATCACTTGUG
F330	433	GATATAGGATGAGUAGCTCCAAATTAATGAAUGT	R330	702	GAAGCCTGUGGTGCTTTTUGCG
F331	434	GAGCTGTAGAAUAGTCAAGAGGAATUGCA	R331	703	GAAAGTCAAACUACACTCAGAACCUGAAT
F332	435	GACTCAGTGCUCTAAATCCAGAGCUG	R332	704	GAGCAAAGGCCAAAGAUAAAATGCTTACUG
F333	436	GAATGAAATATUGTCAACTCTCTUAGGCAAAAT	R333	705	GAAAGCTACAGAAUGTGAACAGTCTTCTUAAA
F334	437	GATACTTUGCAAAGCTGAATUAGACAGCA	R334	706	GAGAGGTAGAUGCTGTAATTGCTGAUACAA
F335	438	GAACATGAGCAUCACATTTTCCTUGG	R335	707	GACAAACACCTCCUGATAAATTGGCTTUG
F336	439	GATGCCTTATGAAUATATTCACGCUGACT	R336	708	GACCCTACUCCAAGGAGCUCAGG
F337	440	GAACCAGGUAAGCACCGAAGUC	R337	709	GACCCAGTUACCATAACTACTCUGAGAAAA
F338	441	GAACCAAGCCGCUGGTUCA	R338	710	GACTTGCAGAGCUATCCCCUAAAGC
F339	442	GAAGACCCCUTTAACTCAAGACUGC	R339	711	GAGCTGCACCGAGUCGTAGUC
F340	443	GAGCGAGGAUATCTGGAAGAAATUCGA	R340	712	GAGTCGUTGTCUCCCCGAAGG
F341	444	GAUTCUCCACGGCCGACCA	R341	713	GAATACAGTCCUGGATGATGATGTTTTUGA
F342	445	GAAAGTCCCUCAAAAATAGGAGGUGCT	R342	714	GAGGACAAGAAAAGUGCAACTUCCCA
F343	446	GAGACAGAUCAGCAACAACCGAAAAUG	R343	715	GATTTCATTGUTTTCCAACUCCGGGAT
F344	447	GATTTGTCCAGAGACCUTTCTAACGTAUT	R344	716	GATTUCCACAGAAACAACAUCGATTTCTTC
F345	448	GATTTCUGAAGAGGACTTGTUGCG	R345	717	GATGCATTUGATCATGCATTUGAAACAAGT
F346	449	GAGATTTTUCAGTTAATAATAUCCCCCGAGCT	R346	718	GAAGTCTGUGCGCGCTUGC
F347	450	GAAATCGCCUCCGGAUCCC	R347	719	GAGTGCGCACGUCGCAAUC
F348	451	GAGTCATTCCTTCUTTTTAAAATGGTGCTUAAGT	R348	720	GAGGATGTAUACAAAAGGCGGATGUG
F349	452	GAGGTCCCCCACCUCTCTTTUG	R349	721	GAGCCAGAGAGUCCCTTUCACC
F350	453	GACTCUCCAGGAAGGCTCACAUC	R350	722	GATGCCACTCUTTGGGTTGAGUT
F351	454	GATGGCATUGCCTTGTCCTUG	R351	723	GATTTCAAACUGGAGGCTTAUCACCAA
F352	455	GAGGCAGAAAACCAAAACAUTGGCTUA	R352	724	GAATACAAGCATGAAAAUCAAAACATATCTTCUGC
F353	456	GAAATTGTTCCTCAAGUTTGTTTAAGGACTUAAAA	R353	725	GAGTAAATGGTAGCTUTTATCATAATCACCAGUC
F354	457	GAAGTGGTATCAUCCCCATTTAATAGCUG	R354	726	GATCCATTCAAGACUTTAGCAGGTGGUA
F355	458	GAACAAATACAAAACUGTCCACATCTATGTUG	R355	727	GAGTTACTCTCATGUGAGAACCATTTGAAUGA
F356	459	GAAACAAACCATAGCUATAATGAAGAACTTGCUA	R356	728	GAGTTTTTCTTATCUCTTAAAATGTTTCTGCUACA
F257	460	GAAATAGTTGATCAUACTTTGTAACAGAAUCACA	R257	729	GAAAGGUACAAGTUAAGGCACACAGAAG
F358	461	GACTCATCTCCCTUTAATTTTGGCACATTAUT	R358	730	GATGGATCTUGGCACAATGAUAACAGG
F359	462	GAAACTATCTUCTTTGGACTTCUGAAGAGAC	R359	731	GATGCTATAGTACCAGUACCTTTTAAGGTUCA
F360	463	GAAGTAAATAATGGTTUCTCCTTCTCTTACTTUG	R360	732	GACCGTAAGGUGGCCTACTTUGC
F361	464	GATTCCTGGUGGCATTCAAUAAAGCA	R361	733	GACAGCGTTTTCUTGTATTCCTGTATTUAGC
F362	465	GAAGGAGCAACUTAGGGATCUGGT	R362	734	GAGGAACTGTGAAUGAACTTGTAGGUG
F363	466	GAACCCCTAAUCTGGTCAACCUG	R363	735	GACCUGACCAGGGCGUCAAA
F364	467	GAAGAAATAGAAAACUACAGGACGTTAUCCAG	R364	736	GAAGTTCATCTUCGAAGCTCAAATTUCAG
F365	468	GATCCGCTTTCUAAAATGTCAGTTGUC	R365	737	GATACAACAAAAUGTTTGACTTCAUGCAGGT

TABLE C

Primer Name	SEQ ID	Primer Sequence	Primer Name	SEQ ID	Primer Sequence
F366	738	AAAACTCAGTAUCAACAACTACCGGUAC	R366	870	TCCCGTGGCUGGTAAATCTGAAAUA
F367	739	CTCAGAAAUGGAAAAAACCTGCAGUAAA	R367	871	CCAAAACATGAAUGTTCTCAACAAGUG
F368	740	GTTCCCTCUGCGTGTTCTCAUAA	R368	872	ATTCCTGCACUAATGTGTTCATUCT
F369	741	AAGAACCTGUGTGAAAGTATCUAGCAC	R369	873	GUCCAAAGCGAGCAAGAGAAUCC
F370	742	AUAAACCAAACCCAUGCAAAAGGAC	R370	874	AGTTCCAGUAGTCCTACTTUGACACT
F371	743	GCATTGAUGGAAGGAAGCAAAUACA	R371	875	AGAGCACGTUCTTCTGCTGTAUG
F372	744	CCAGCTTCAUAGACAAAGGTTCUCT	R372	876	AGTTGAATATCTGTTUTTCAACAAGTACATTUT
F373	745	GTGGTTTCTUCCATTGACCACAUC	R373	877	GCCTGGCCUGAATGCCTUAAA
F374	746	CAAAUGGGCAGGACTCTUAGGT	R374	878	CAATTTCAACACAAGCUAAACTAGUAGGAT
F375	747	GUGAGGAAACTUCTGCAGAGGT	R375	879	TCAACAAAAGUGCCAGTAGUCATTTC
F376	748	GGAAGCAGGGAAGCUCTTCAUC	R376	880	CTGTTTTUAGCAAAAGCGUCCAGA
F377	749	TGGTTUGAAGAACTTTCTUCAGAAGCT	R377	881	AGTCAGCCCUTGCTCTTUGAAT
F378	750	AGGGAGACUGUGTGTAATATTTGCG	R378	882	TTGGCCAUACAAAGTGAUAAAGGACTT
F379	751	GCCAGTATUGAAGAATGTTGAAGAUCAAAA	R379	883	TTTGCAGGGUGAAGAGCTAGUC
F380	752	GCCAAAAGGAAGUCTGTTUCCAC	R380	884	TGTACAAAUGGGACTAACAGGUGGA
F381	753	CATGCCACACAUTCTCTTTTTACAUGT	R381	885	AGCATACCAAGTCUACTGAATAAACACTUT
F382	754	GTAGAGUGCTACACTGUCCAACA	R382	886	CCTGGAGTCGAUTGATTAGAGCCUA
F383	755	CTCTGAGAAAGAAUGAAATGGAGTUGGA	R383	887	AATGTGTTATGUGGCTCCATTATUAGCT
F384	756	AAACAAATTTUCCAGCGCTTCUGA	R384	888	GCATTTTTACCUACGATATTCCTCCAAUG
F385	757	AGCAATAAAAGTGUATAAATGCCTGTAUGC	R385	889	ACCAGTAAAAAUAAAGAACCAGGAGUGG
F386	758	TCAACAAGTTGACUAAATCTCGTACTTUCT	R386	890	TTATAGAGGTTTUCTACTGTTGCUGCAT
F387	759	CATTCTTACAUAAAGGACACTGUGAAGG	R387	891	GCAGTTGTGAGAUTATCTTTTCAUGGC
F388	760	CCCTTACAGAUGGAGTCTTTUGGC	R388	892	CATCATTCACCCUTGGCACAGUAA
F389	761	AAAGACCTTTUGGTAACTCAGACUCAG	R389	893	AAAUATTTTCTAGGAATUGCGGGAGGA
F390	762	ACATTCACUGAAAATUGTAAAGCCTATAATTG	R390	894	CAGGUAAUCGGCTCTAAAGAAACATG
F391	763	GGTTGTGCTTTTUAAATTTCAATTTTATTTTUGCT	R391	895	CAGAGAGATUCGAGGCAGAGUG
F392	764	GGATGUCACAACCGUGTGG	R392	896	AGTAGUGGATTTUGCTTCTCTGATATAAACT
F393	765	AGTGAAAACUAAAATGGAUCAAGCAGATG	R393	897	GCTCTUAGCCAAAATATUAGCATAAAAATCAG
F394	766	AAACTAGTTTTUGCCAGTTTTTUAAAATAACCT	R394	898	AAAAAGCATUGTTTTTAATCAUACCTGACTT
F395	767	TTTTTACCCCCAGUGGTATGUGG	R395	899	GGTACAGAUTTGTAAATCUCAGGGCAA
F396	768	GAAAACACAAAUCAAAGAGAAGCUGCA	R396	900	GAGAUCACGGGUGACAGAGC
F397	769	ATATTTAGUAGCCAGGACAGUAGAAGGA	R397	901	ACCTACCTGAUACCCCAGAUCCC
F398	770	AAATATTTCAGUGTCCGTUCACACACAA	R398	902	TCCAGATTGAUCTTGGGAGTGUAAAAA
F399	771	GCAGAUGCAAGGTATTCTGUAAAGG	R399	903	GTGTGCTAGAGGUAACTCATGATAAUGG
F400	772	ACCTACATAAAACUCTTTCCAGAATGTUGT	R400	904	GAAAGGGUCAACAAAAGAATGUCCAT
F401	773	CCCTTTCTGTUGAAGCTGTCAATUC	R401	905	GAAAGTTCCCCAAUTGAAAGTUGCAG
F402	774	AGAUGGTATGTUGCCAACACGAG	R402	906	AACTTTGTAATUCAACATTCATCGTTGUGT
F403	775	GATGTTTCCGUCAAATCGTGUGG	R403	907	TAGATGATAGGUGGTACATGCACAGUT
F404	776	GTAGAACTATCUGCAGACACCUCAAAC	R404	908	ACCUGAATTATCACTAUCAGAACAAAGCA
F405	777	CCAGAACCACCAUCTTTCAGTAATTUG	R405	909	GAACAGUACCCGTTCCCTUGA
F406	778	ATCATAAAATGTUGGAGCTAGGTCCUT	R406	910	CTTGAGGACCUGCGAAAUCCAG
F407	779	TATGATGGAAGGGUAGCTGTUAGAAGG	R407	911	TGGAAAGCTTCUCAAAGTATTTCATTTUCT
F408	780	GGTTAAAATGTCACUCTGAGAGGAUAGC	R408	912	GCAGCGTTTAUAGTCTGCTTTTACAUC
F409	781	GGAAATTTGUAAAATGTGCUCCCCAAA	R409	913	AACGGGCTUGGAAGAAAATAAUCAAG
F410	782	AATTCCTTGTCACUCAGACCAACUC	R410	914	TCTGCTAGCUTGTTTTCTUCACAGT
F411	783	ACTAAGGTGAUGTTCCTGAGAUGC	R411	915	AACAATATACCTUCTCAGTCTACUAGGCAT
F412	784	ACTTTCCUTAATGTCATTTUCAGCAAAACT	R412	916	CAGATAACTUAGAACAGCCTAUGGGAAG
F413	785	CAGTCTGAACUACTTCTTCATATTCTUGCT	R413	917	GGCCAAAATUGAATGCTATGCTUAGAT
F414	786	CTAGTTCTGCUTGAATGTTTTCAUCACT	R414	918	AGCACAATUAGCCGTAATAACATUAGAGAA
F415	787	TGGAATGTTCTCAUTTCCCATTTCTCUT	R415	919	TGGACTCATTACUCCAAATAAACAUGGA
F416	788	GTTTCGTUGCCTCTGAACUGAGAT	R416	920	GTCTAATATCAAGCCUGTACAGACAGUT
F417	789	CCTTGATTTTCTUCCTTTTGTTCACATUCA	R417	921	TGCAGAATACAUTCAAGGTTUCAAAGC
F418	790	TTTCTATGCTUGTTTCCCGACUGT	R418	922	AATAAATGTGUGAGTCAGTGUGCAG
F419	791	GAUGAAAGCTCCTUCACCACAGAA	R419	923	AAGCCTTCAUCCGGAGAGTGUA
F420	792	CCTAGAGTGCUAACTTCCAGUAACG	R420	924	TAATGCUGAAGACCCCAAAGATCUC
F421	793	CTTGGAAGGCUAGGATTGACAAATUCT	R421	925	GCCAAAUGAACAGACAAGUAAAAGACA
F422	794	TTGTTACTCTTCUTGGCTCCAGTUG	R422	926	GCAAATTGATAGUTGTTCTAGCAGUGAA
F423	795	TTAGGTGGGCUTAGATTTCTACUGACT	R423	927	CAGCAGTAUAAGCAATATGGAACUCGAA
F424	796	TGCTTATAGGTUCAGCTTTCGTTTUG	R424	928	GGAGCAGAATGGUCAAGTGATGAAUA
F425	797	CCACTATGUAAGACAAAGGCUGGT	R425	929	TTTTATAACTAGATTTUCCTTCTCTCCATUCC
F426	798	TCCGTTTGGTUAGTTCCCTGATTTAUC	R426	930	AGAGCGTCCCCUCACAAATAAAUT
F427	799	GTATTATCTGUGGCTCAGTAACAAAUGC	R427	931	GAAAGAGTTCACUCCAAATCAGUAGAGA
F428	800	TTAAAGCCTCAUGAGGATCACUGG	R428	932	GGTTCTGAUGACTCACATGAUGGG
F429	801	AGTTCATCACTUCTGGAAAACCACUC	R429	933	CCCTGTGUGAGAGAAAAGAATGGAAUAA
F430	802	GGGATCAGCATUCAGATCTACCTTTUT	R430	934	AGGCUGAATTCTGTAAUAAAAGCAAACA
F431	803	TTCAGCCTTTTCUACATTCATTCTGUCT	R431	935	AGGGTAGTTCUGTTTCAAACTUGCAT
F432	804	TACCCTGAUACTTTTCTGGAUGCCT	R432	936	TGTATATTTTCAGCUGCTTGTGAATTTUCT
F433	805	GAATCCAAACUGATTTCATCCCUGGT	R433	937	GACAGTTCTGCAUACATGTAACTAGUGT
F434	806	AGCTGCCUACCACAAATACAAATTAUG	R434	938	GCGGAUACAACCUCAAAAGACG
F435	807	CAGAGTTCUCACAGTTCCAAGGTUAG	R435	939	TGUCAAGTTTCTCTUCAGGAGGAAAAG
F436	808	GAAGAAGAAGAAAACAAAUGGTTTUACCAAG	R436	940	AAGGAAAATAACUCTCCTGAACATCUAAAAGA
F437	809	ATCACCACGTCAUAGAAAGTAATTGUGC	R437	941	TGTTGAAGAGCUATTGAAAATCATTTGUGC
F438	810	CATTCAAACTTACTUGCAAAATATGTGGUC	R438	942	ACAGCTCAAAGUTGAACTTATTCACUAAGA
F439	811	GCATAGGAGATAAUCATAGGAATCCCAAAUT	R439	943	ATGTTTTTCTAATGUGTTAAAGTTCATUGGA
F440	812	AGTTGTAGTTGTUGAATTCAGTATCAUCCT	R440	944	GCCAGTTTCCAUATGATCCATCTAUAGT
F441	813	TGTGCCTTTCCUAAGGAATTTGCTAAUA	R441	945	AGAAACCTTAACCAUACTGCCGTATAUG
F442	814	AAAAGATAAUGGAAAGGGAUGACACAGC	R442	946	GCCACTTTTUGGGTATCTGCACUA
F443	815	CTGTTAAGGCCCAGUTAGATCCUC	R443	947	TTCAAGAGGUGTACAGGCAUCAG
F444	816	AGGCAGTTCUAGAAGAATGAAAACTCUT	R444	948	GGTCAGGAAAGAAUCCAAGTTTGGTAUA
F445	817	TGTACCTAGCAUTCTGCCTCAUAC	R445	949	CCTCAGCTCCUAGACTTTCAGAAATAUG
F446	818	TAGACCTTTTCCUCTGCCCTTAUCA	R446	950	AAACTCCATCUCAAACAAACAAACAAATUAAT
F447	819	CACATUATTACAGTGGAUGGAGAAGACA	R447	951	CCTCCTGAATTTUAGTGAATAAGGCTUCT
F448	820	CTTCTTTGGGUGTTTTATGCTTGGUT	R448	952	GCAAAGCACGAACUTGCUGT
F449	821	GCAGAGCTUTATGAAGCAGUGAAGA	R449	953	GTGAUGGCCAGAGAGTCUAAAACAG
F450	822	TCTTAAATGGUCACAGGGTTATTUCAGT	R450	954	TGACATCCCTUGATAAACCTTGTUCC
F451	823	TTCCATTGCATCUTTCTCATCTTTCUC	R451	955	TTTTTGTCGCUGCTAACTGTATGTUA
F452	824	TTCACTUCAGCAAATTTTTAGAUCCAGAC	R452	956	GCTCCAACTAAUCATAAGAGATTTUAAAAGAC
F453	825	TGCCCCTTUCGTCTATTTGUCAG	R453	957	AAGTAAGAAGGCCUGATTTGGATUCT
F454	826	GGAGATTTTTCTGUGTTTTCTGCTAGUC	R454	958	GCTATTTCCTUGATACTGGACTGUCAAA
F455	827	TGACAUACTTTGCAAUGAAGCAGAAAA	R455	959	ATTCCTTGAGUTTACATTAACTUACCAGAAG
F456	828	GGATCCTGATAUGTCTTGGTCAAGTUC	R456	960	ATGACAATTATCAACCUCATCTGCTCUT
F457	829	GGCACCAAAUACGAAACACCCAUA	R457	961	TAAATTGUTTTTCTCCTGTUGAACCAGACA
F458	830	ATATCTGTCAGTGAAUCCACTAGGACUG	R458	962	CCTGCTTATTTUTCTCACATTCTUCCG
F459	831	TGAAGAAGCAUCUGAAACTGTATTTCCT	R459	963	GGTTUAGAGACTTTCUCAAAGGCTTAGAT
F460	832	GGACTACTACTATAUGTGCATTGAGAGTTUT	R460	964	GTGTTTUCACTGTCTGUCACAGAAG
F461	833	TGGCTTATAAAATATUAATGTGCTTCTGTTUT	R461	965	AAAACTATCTTCUTCAGAGGTATCUACAACT
F462	834	GGTAAAAAUGCCTATTGGAUCCAAAGAG	R462	966	GTGACGUACTGGGTTTTUAGCAAG
F463	835	AATCTACAAAAAGUAAGAACUAGCAAGACT	R463	967	GGCTTCTGATTUGCTACATTTGAAUCT
F464	836	AAGTGACAAAATCUCCAAGGAAGTTGUA	R464	968	AGGTCTTTTTCTGAAAUATTTTGGTCACAUG
F465	837	GAATTCTTUGCCACGTATTTCUAGCC	R465	969	AGATATTGCCUGCTTTACUGCAAGAA
F466	838	GGCTTCTTCAUTTCAGGGTAUCAAAAA	R466	970	TGTATTTCCAGUCCACTTUCAGAGG
F467	839	AATACAUACTGTTTGCUCACAGAAGGAG	R467	971	TTGTTTTCTTTTUCAAAGTGGATATUAAACCT
F468	840	ACCGAAAGACCAAAAAUCAGAACTAATUAAC	R468	972	CAGAAGGAATCGUCATCTATAAAACTATAUGT
F469	841	TCACAGAAUGATTCUGAAGAACCAACT	R469	973	CTGTAGTTTTTCCTUATTACATTTTGCTTCUT
F470	842	ATTACCCCAGAAGCUGATTCTCUGT	R470	974	TGGGATTGAAAGUCAGTATCACTGTAUT
F471	843	TATATGATCATGAAAAUGCCAGCACUCT	R471	975	GTTACCTTTGAGCUTGTCTGACATTTUG
F472	844	TTCCCATGGAAAAGAAUCAAGATGTAUG	R472	976	TTGGATTACTCTUAGATTTGTGTTTTGGTUG
F473	845	ACTGTCAATCCAGACUCTGAAGAACUT	R473	977	ATGGTAGAGTTCUTGAAAATGGGTUC
F474	846	CAGGUGAUAAACAAGCAACCCAAGT	R474	978	GTATTTTATCTATATUCAAGGAGATGTCCGAUT
F475	847	TGGCATTAGAUAATCAAAAGAAACUGAGC	R475	979	GCCTTTTGGCUAGGTGTTAAATTAUGG
F476	848	GAATCAGGAAGUCAGTTTGAATTTACUCAG	R476	980	GTCTACCUGACCAATCGAUGGG
F477	849	GCCTGTUGAAAAATGACTGUAACAAAAG	R477	981	AGCTTTTUGCAGAGCTTCAGUAGA
F478	850	TGAAGATAACAAAUATACTGCUGCCAGT	R478	982	GGCCAGATAATTUAAGACATATGTTGUGC
F479	851	AGGAGGGAAACACUCAGATUAAAGAAGA	R479	983	GCTCCGTTTUAGTAGCAGTTAACUGT
F480	852	TTTCAGACTGCAAGUGGGAAAAATAUT	R480	984	GTCTGTTTCCUCATAACTTAGAATGUCCAT
F481	853	TCTTCTTACAACUCCCTATACATTCTCAUT	R481	985	TCACTGTGCGAAGACUTTTATGTCUA
F482	854	CCAGTTGGTACUGGAAATCAACTAGUG	R482	986	TTTCACTTTGUCCAAAGATTCCTTUGC
F483	855	AAAAGAGCAAGGUACTAGTGAAAUCACC	R483	987	AGAATTCTGCAUTTCTTTACACTTUGGG
F484	856	AAAAACCTTGTTUCTATTGAGACTGUGG	R484	988	GGACTGATTUGTGTAACAAGTUGCAG
F485	857	AATTCAGCCTUAGCTTTTTACACAAGUT	R485	989	TCATACAAATAATUTCCTACATAATCUGCAGT
F486	858	TGACAAAAAUCATCTCUCCGAAAAACAA	R486	990	CAATACTGGCUCAATACCAGAAUCAAGT
F487	859	AATAATTTTGAGGUAGGGCCACCUG	R487	991	AACCTGCCAUAATTTTCGTTUGGC
F488	860	TCATAACTCTCUAGATAATGATGAATGUAGCA	R488	992	GAAGTTTCCAAACUAACATCACAAGGUG
F489	861	GTATAGGGAAGCUTCATAAGTCAGTCUC	R489	993	ATTTCAGAAAACACUTGTCTTGCGUT
F490	862	AGAAGATAGUACCAAGCAAGTCTTTUCC	R490	994	ACCACATTATAUGAAAAGCCTTTTUGGG
F491	863	TAGTACAGCAAGUGGAAAGCAAGUT	R491	995	GGUTTCTCTTAUCAACACGAGGAAGT
F492	864	CAGGCTTCACCUAAAAACGTAAAAAUG	R492	996	CTGTCAGTTCAUCATCTTCCAUAAAAGC
F493	865	ATGAAATAUTTCTTTTUAGGAGAACCCTCAAT	R493	997	TATACCAUACCTAUAGAGGGAGAACAGATAT
F494	866	ATATATTUTCTCCCCATUGCAGCACAA	R494	998	GCTTGAAGATTTUTCCAAAGTCAGAUGT
F495	867	AGGACATCCAUTTTATCAAGTTTCUGCT	R495	999	GTTTTGCTTTUGTCTGTTTTCCUCCAA
F496	868	TGGCTCTGATGAUAGTAAAAATAAGATTAAUGA	R496	1000	AGGCAAAAATTCAUCACACAAATTGUCA
F497	869	GCTGTATACGUATGGCGTTTCUAAACAT	R497	1001	TCATTGGAGGGUATGAGCCAUCC

TABLE D

Primer Name	SEQID	Primer Sequence	Primer Name	SEQ ID	Primer Sequence (target of PrimerC)
F498	1746	GAGUGUGCGUGGCUCUCA	R498	1275	UGCCAUCAU UCU UGAGGAGGAAG
F499	1002	ACAACUGCAGCAAAGACUGGT	R499	1276	UGCAAUCCCUGCCCCGGUT
F500	1003	AGUUAAUUUUGGUUACAUCCCUCUCUGC	R500	1277	GGAUUGCAGGCUCACCCCAAT
F501	1004	AUCGAUCUGUUAGAAACCUCUCCAG	R501	1278	CUGGAUUUCCUCAUGGAAGCC
F502	1005	GGACUCUGUAGGCUGCAGT	R502	1279	AAAUCCAGUUCGUCCUGUUCA
F503	1006	UGAGGCAGUCUUUACUCACCUG	R503	1280	GAAACUGCCUCUUGACCUGUCC
F504	1007	ACAAGCAAAGUCUCUAUGGUGAUUAUGT	R504	1281	AGGACAGUCAUGUUGCCAGUAUUAAAAT
F505	1008	CAAC UACCAU CCAGCAACAGAAAAT	R505	1282	CUUCCAUGACUUUGGCAAUCUGG
F506	1009	GACAGAUGAGAGAAAUGCACUUAGAAGA	R506	1283	GAACAUGUCCUAUUUGAAUUUUCCGACUT
F507	1010	AGGAAUGUGUUUCUCCAUACAGGUC	R507	1284	GACACAAAGACUGGCUUACAUUUUGAT
F508	1011	CUUCAAGCAGUGAGAAUACGUCCA	R508	1285	AGGCUGACCACUUCUACUCUGT
F509	1012	AGGGUCCAGGUUCUUCCAGA	R509	1286	GCACUCAGGCUGGAUGAACAA
F510	1013	GAUAGUUUUGAGAGUCGUUCGAUUGC	R510	1287	UGUCCAGGGCUAUCUGGAAGAUC
F511	1014	CUCCACCACCUCCUCAAACAG	R511	1288	GCAGCAUUUACUGCAGCUUG
F512	1015	AUCAGCCAGGCACAAAGC	R512	1289	UGACAGAAGUACAUCUGCUAAACAUGA
F513	1016	CAUCUUUGUCAUCAGCUGAAGAUGAAAT	R513	1290	CUCACAGGAUCUUCAGCUGACC
F514	1017	GCCUAAAGAAUCAAAUGAAAACCAAGAGA	R514	1291	ACUUUGUUGGCAUGGCAGAAAT
F515	1018	GUGACCCGGAGCACUUCC	R515	1292	GCCGUGGUGCUGACCAT
F516	1019	CCACAUUACAUACUUACCAUGCCACT	R516	1293	GUGAUGAUUGGGAGAUUCCUGAUG
F517	1020	AUGGGACCCACUCCAUCG	R517	1294	GCUCUGAUAGGAAAAUGAGAUCUACUGUT
F518	1021	CCCUUCUAAGGACCCCCUCUUC	R518	1295	CUCCAGCAGGGCUUCGAT
F519	1022	CUCUGCCGGGCUUUGAUCUT	R519	1296	GGACUUUGCAACUUCAACAAAACUC
F520	1023	UACUACCGCCUCACACGCT	R520	1297	CUAGGUGUCUCCCCCUGUAAG
F521	1024	UUCCCUCUCUCCUUCUGCCUC	R521	1298	AGGUUCAGGCCUUGCACT
F522	1025	CCAGCAGAAGACAAAAAGACAAACA	R522	1299	CCAGCCCAGGAAGCAAAGAG
F523	1026	GGAGAGGGAGGAGAGCUAACT	R523	1300	UUAAAACUGGUCUCGCUCUCCC
F524	1027	AGAAGCUGUGCAUUUACACCGA	R524	1301	GAAAGCGGGAAUCGCAGAAA
F525	1028	UUUUGCUGAUGCUAUGCUCUCCAC	R525	1302	GGAAGACCUCUUCUUCGCACUT
F526	1029	CUGAUCCGCAAGCAUGCUC	R526	1303	CAAAAGAGCUCCCCCAUCUCC
F527	1030	UGAGCUCGCUCACUUGUGAUG	R527	1304	AGAAGAGACAUCUGGACUUAGCCAA
F528	1031	CAGGAUCCAAAUUCGUUCUGUGC	R528	1305	AUCAUCGACGGUGGGUACAUG
F529	1032	UACUAACAACUCUGGUCUGGACCAT	R529	1306	CGUUGGUCCUGACGGUACUG
F530	1033	AUGCUAUUUGGACAAUAAACUCACCUUG	R530	1307	CCAUUCUGAGGACUGCUGGUUUAUA
F531	1034	CUCCUUACCUCAUACAGUGCAGAAA	R531	1308	CCAGGACCAUCAUCCUACUGUAA
F532	1035	CCCUGAGUGCAGCUUCGAUC	R532	1309	GAGUGUUUGCUCCUCACUCUUC
F533	1036	CGAUCAUGGAUGGCGGGUAC	R533	1310	CUUCAGGUUUCCUUCUCUCAUGGUT
F534	1037	UUUAUGAAUGGAGAGGCUGCUG	R534	1311	GGAUGAGCUCACAGAGCUGC
F535	1038	ACCUCUCACCCUUAUAAGUCUUCUGA	R535	1312	UCAAAAAGCAUGCCCAGACCUUT
F536	1039	ACUUGAGCUUCCCUAGGACCA	R536	1313	ACUUUGAGACUUCUGCUUUGCUC
F537	1040	GGGAGACAAUACGUGUCGGG	R537	1314	AUCGAAAAACUGUGCAUCUACACC
F538	1041	AAGACAGGUAGCGAUCCAGGUAG	R538	1315	AGACCCAGCAGUGACUGT
F539	1042	CUAGGUGCCCAUGUCCAUCUG	R539	1316	ACAAGUAUAAUGAGCACCCCUUCT
F540	1043	GAUGUCCAAUGUACCUGAGGCAA	R540	1317	GUGGACACACCUGUAUUCCUGAG
F541	1044	CAGCAGAAAGAGGACUCAGAAUAGAAAAUC	R541	1318	CCGACCAGUUGGGCAAAAUC
F542	1045	AGAGAUUCGCUUGUGUGGGUUAAA	R542	1319	GCAGAAGUCUGUUUUCUUCAUGGUT
F543	1046	ACCAGGGUUACCUUGAUCUCC	R543	1320	AGGCCAUGUUGGGUUAAAGG
F544	1047	ACUUCUCAAUUGCUACGGGCAAUC	R544	1321	AGAAUCUACAGCUACCAGAUGGCA
F545	1048	AGAUCUCGGUGAACGAUGCAAT	R545	1322	CCUAGUUUCCAGUGCAUCUGUACC
F546	1049	UAUGUGGACUGCAGAAGAACUUCG	R546	1323	GGUCCCCAUCCAUUCUUCCUAUUC
F547	1050	UGUGGUUUAUGAACAAGCGAUUUGG	R547	1324	UGUGGAGUGUUGGCUGUAUCUUUG
F548	1051	GCUCAUAUCGAGAGGUAGCCAUUC	R548	1325	CUCUGUAAGCGACUUUUGGUGAUAG
F549	1052	GCAGACGAGCUUGACAUCAGAAA	R549	1326	GCCCAACCAAUUGAGAAGUUUGUAA
F550	1053	AAGACUUCGGGUGCUCUGUAC	R550	1327	UUAGUCAGGAGUCUAAGCCAACAG
F551	1054	GGGACAGACUGUCAUUCAAAAUAGGA	R551	1328	CUUGCCCGCAUCUAUAGUUUCCA
F552	1055	UGAAGAAAGUCCAGACCUCGGA	R552	1329	AACUUCCGUUUUGAGUGUUUACUGAUUT
F553	1056	GUCGACUGCCUGAUAAGACAUGA	R553	1330	UUACUUGGAUAAAGUUCCAGAGCCT
F554	1057	UAGUUUGGUUUCUCUGUCUGUUCGUG	R554	1331	GCUUAUUGCCACCUACUUAACCUCT
F555	1058	AAGCCUCCAUCGCUACCCT	R555	1332	CUUCAGCCCUGCAGGGAAA
F556	1059	UCAGGCGCCAAGUAGGT	R556	1333	GGCAAGUUCAACAUUAUUCCCUUUUGUA
F557	1060	AAAGCGGCUGUUAGUCACUGG	R557	1334	UCUUCCUCAGGAUUGCCUUUACC
F558	1061	UAAAGAUCAUGUCUCGGCUCAAGGA	R558	1335	CAUACAGAGAGGGUCAUCAGUGAUAC
F559	1062	GUGCACAGGUUAUUCUGAUUUCCC	R559	1336	GAAAGUCUCCCACAAAGUAACCC
F560	1063	AGAAGGGCUAGGCCAAUUGAC	R560	1337	AUAGUCAUAGCCGGGCCACA
F561	1064	GUCAGCCUGAACAUAACAUCCUUG	R561	1338	CCAGUUUAUUGUAUUUGCAUAGCACA
F562	1065	GGGACCUCCGGUCAGAAAAC	R562	1339	GGACCCAUUAGAACCAACUCCAUAAA
F563	1066	CUCCCAACCAAGCUCUCUUGA	R563	1340	UACCUUAUACACCGUGCCGAA
F564	1067	CCCAGAAGGUGAGAAAGUUAAAAUUCC	R564	1341	CCACACAGCAAAGCAGAAACUC
F565	1068	AGGGCAUGAACUACUUGGAGG	R565	1342	UUCUUUCUCUUCCGCACCCA
F566	1069	GCCUCUCCCUCCCUCCAGGAA	R566	1343	GUGAGGCAGAUGCCCAGCA
F567	1070	UGCCUCACCUCCACCGT	R567	1344	CCAAUAUUGUCUUUGUGUUCCCGGACA
F568	1071	AAGUGUAAGAAGUGCGAAGGG	R568	1345	UGUGUUCCUUUGGAGGUGGC
F569	1072	GCCUUUUUAACUGGUAGAGAUUGGUG	R569	1346	GAUCCAGAGGAGGAGUAUGUGUGA
F570	1073	UCAUCACCUUCCUUUCAUGCUCUC	R570	1347	UCUUCCUCCAUCUCAUAGCUGUCG
F571	1074	UCCUACGUGGUGUGUGUCUGAA	R571	1348	CGUCCUGUUUUCAGGCCAAG
F572	1075	UGAUCAUCGAAUUCUCCAAAAUGGC	R572	1349	AUUAGAGGGACUCUUCCCAAUGGA
F573	1076	GAUGAGAUGUGGUACAAGCAUUCCA	R573	1350	CCACGGUGGAAUUGUUGCUG
F574	1077	CCCCUACAGCAUUGUUAAGAAAGUAUUT	R574	1351	AUACCAGGCUAGUAUAGAUGCUUAGGG
F575	1078	CUGGGACUAGCAUGCUGACC	R575	1352	CAGACACCAACUCCCGGAAUC
F576	1079	CUGCCUGUCUCUGGUUCUGT	R576	1353	CAGAACUCUCUCCCCAGCAG
F577	1080	ACUUGGAGUGAGUUUGGAUGGG	R577	1354	CAGCUUCAUGUCUGUGCCG
F578	1081	UCCUGAUCUCCUUAGACAACUACCUT	R578	1355	UCACACCGCUGUGUUCCAUC
F579	1082	UGUUCCUAUUUCAGCCCCACUC	R579	1356	GUUGUGAGCGAUGAGCACGUA
F580	1083	GGAAAGGGUCCUCUGAUCAUUGC	R580	1357	AAAAUCGUGUCCUGGUAGCAGAG
F581	1084	CGAGGGCCGGUAUACAUUCG	R581	1358	CCCACCAAAAUGAGAAAACUGUGUT
F582	1085	GAAUGUGAAAAUUCCAGUGGCCAT	R582	1359	UGUCCUCCUAGCAGGAGAGG
F583	1086	AUACCCUCUCAGCGUACCCUT	R583	1360	CCGUGGAUGUCAGGCAGAUG
F584	1087	AGCGCUUUGUGGUCAUCCA	R584	1361	AUACUGGACUCAUCUCUCCUUCCC
F585	1088	AAACUAGCCCUCAAUCCCUGAC	R585	1362	AAAGACCACCCCCAAGACC
F586	1089	CACAGUUGGAGGACUUCCUCUUC	R586	1363	AUAACUCCACACAUCACUCUGGT
F587	1090	CUACAUGGGUGCUUCCCAUUCC	R587	1364	UUGACAUGGUUGGGACUCUUGAC
F588	1091	GUCCUCGUGGCCAUGAAUGAA	R588	1365	UGGCAAACUUCCCAUCGUAGAC
F589	1092	CCCAAUCCCCACACCAAGUAUC	R589	1366	GUUGAUCAUUGUUCCUUCCCCUCA
F590	1093	AUGUUCCUCCCUCAUCUCUAAUGGT	R590	1367	CCAUCUUGUCAGGAGGACAGG
F591	1094	UGGACUCGAGCAACAUUGAUGG	R591	1368	GGCAGGAUCUCUAACCCAUUGAG
F592	1095	GCUGAAGUACCAGACCUGCUA	R592	1369	CUCAGCAGGUAACUCACACUUG
F593	1096	GGAUUUGACCCUCCAUGAUCAGG	R593	1370	CUUCCCUGGGUGCUCCAT
F594	1097	UCACUCUCUCUCUGCGCAUUC	R594	1371	GUGGAUAUGGUCCUUCUCUUCC
F595	1098	CAUGAAGUGCAAGAACGUGGT	R595	1372	GGCUAGUGGGCGCAUGUAG
F596	1099	GCGGAUCAGAGCCUCAAAC	R596	1373	AUCAAAGUCCAGCACCAGCA
F597	1100	ACUGUCCUGUUUUGAUAUCCCAGAUUUT	R597	1374	GGGAAUUGCAUUCACACGUUAACA
F598	1101	CUGUCUCAAUAUCCCAAACCCUAAG	R598	1375	UUUGUUUUGUUUUUCUGUUUCUCCCUCUG
F599	1102	UAUUAGUAUGCCCCUGCAACGUG	R599	1376	GAGGGUUGUUAGUGGAGCAUAUGA
F600	1103	CAACCCUCCUGCCAUCAUAUUGA	R600	1377	UGAGACAGGCCAGUGUUUACAUG
F601	1104	CAACCAUGACAAGAUUUUCCCUUACC	R601	1378	GAGACUGGAGAAUGUAUACACACCUT
F602	1105	UGCCUGUGGAGGAACUUUUCA	R602	1379	CGACAUCUCCUCGGGCUT
F603	1106	CUUCCUCUCGCCCAUCACA	R603	1380	CGUAGAGCUCCGGGUGUC
F604	1107	AGUGCCUCCUCUCCCAUCUT	R604	1381	CUACCCAGGGCCACUGUUUT
F605	1108	CACUCCUUGCUUCUCAGAUGAAACC	R605	1382	GGGACAUUCACCACAUCGACUA
F606	1109	CAGGUACUCCCGCAGGUUG	R606	1383	UGGCCUCUUCUCCUGUGC
F607	1110	CACGCAUACGGUUUGGUUUGG	R607	1384	CUUCUUCUUCCCAUAGAUGCUCUCC
F608	1111	CUAGAAGCUCUCUAUCCCACACCT	R608	1385	GAGGCAUUAUUUGACCGGAUCUAC
F609	1112	CAAGGAAUGCCUUCAAAAAGUUGGG	R609	1386	CUGAGUAUGAGCUUCCCGAAGAC
F610	1113	AGAUGAUGAUCUCCAGGUACAGG	R610	1387	CCUGCUAACACCCUGUUCG
F611	1114	CGGCACUGCAUGCAAUUUCUT	R611	1388	CUGCCUGUCUCUCUUGGCUUT
F612	1115	CCAUUUAUAGCUGAGUCUCCAUCCUG	R612	1389	UAUGAACUUCCAGAGGACCCAAAAUG
F613	1116	CCCAGUUGUGGGUACCUUUAGAT	R613	1390	GGAAAAGAACGGCAGUAAAUACGG
F614	1117	CUUUCAAACGAGUCAAGCAAGAAUGG	R614	1391	AAUACGGGUCCAUCAAUCACACG
F615	1118	ACCACACUUUCCAUAAUGAGGCT	R615	1392	CAGUACUUGGUAUUCUGUGCUAGGA
F616	1119	CUUUUCCAUCUUUUCUGUGUUGGUC	R616	1393	GGAAGCUGUCCAUCAGUAUACAUUC
F617	1120	CAGACAAAU CCCAAAACAAACC UGA	R617	1394	GGCCCUCCUUCAGUUUAGUUGAG
F618	1121	GUAGCUACAGGACUCAGAUACGUG	R618	1395	GGUGGAGGCGAUAGUGGAUAG
F619	1122	GUAUUUGGGCGAAUGCAGUUUUUC	R619	1396	AGAUGGAGAUGAUGAAGAUGAUUGGG
F620	1123	CCAGAGAAAAGAGAGUUACUCACACA	R620	1397	GUCAAGUGGAUGGCUCCAGAAG
F621	1124	ACUGUGUUACUGCCAUCGACUUAC	R621	1398	CCAGAAAUGUUUUGGUAACAGAAAACAA
F622	1125	GGUAUUCUCGGAGGUUGCCUUT	R622	1399	AUUCUCUCUUUAGGGAGCUUCUCUUC
F623	1126	CUUGGUCGUGUUCUUCAUUCGG	R623	1400	UGGAAGAGAAAAGGAGAUUACAGCUUC
F624	1127	ACCACUGUGGAGGCAUUUG	R624	1401	AUUGGUCUCUCAUUCUCCCAUCC
F625	1128	AGUGAAGAUCUCCCACAUUAACACC	R625	1402	GUUUAGGUUUUGGCAACGUGGAT
F626	1129	CU UGCCCAAAGCAACCU UCUC	R626	1403	UCACCAGAUGCUAUGUGCUAAUCC
F627	1130	AUUGGUUGCGGCCAUCUCT	R627	1404	UCCUACCUGUGUCCACACC
F628	1131	ACCAAUUUCAUAGGCGUGGC	R628	1405	GGCAUGGGACAGAGUCGUT
F629	1132	GCCUAUCGCUCUGCUCUCUC	R629	1406	UUGUGCAAGGAGAGAACCUCUA
F630	1133	UAACCCAGCGACGAACUUUCC	R630	1407	CCUAUCCCAGAACUGGAGACAGAAA
F631	1134	GCCCCUGAGCGUCAUCUG	R631	1408	UGUACACCUUGCAGUGGAACT
F632	1135	CUGGUGGAGGCUGACGA	R632	1409	AGCCCAGGCCUUUCUUGG
F633	1136	ACAACGUGAUGAAGAUCGCAGA	R633	1410	ACUGGCAUGACCCCCAC
F634	1137	GGGAGAUCUUCACGCUGGG	R634	1411	UGCCACUCACAGGUCGT
F635	1138	GUCUGAGGAGCCCGUGT	R635	1412	GCAGAAACUCCCGCAGGT
F636	1139	UCCUCGGAGCAGUGAGGG	R636	1413	ACUCCAGAUACUGCAUGCCT
F637	1140	AGCCUCUCCACGCUCCCUC	R637	1414	ACUCCCGCAGGUUUCCC
F638	1141	CUCACAUUGCCCCUGACAACAUA	R638	1415	ACGGGAAAGUGGUGAAGAUAUGUG
F639	1142	GUGUCCUUUCAGGAUGGUGGAUG	R639	1416	AGAAACAUGAUGGAUGUCACGUUCUC
F640	1143	GGUGACAUUUUCAAAGCAGUGUAUCC	R640	1417	UGUUAACCUUGCAGAAUGGUCGAT
F641	1144	GGGUAUUCGAUGAUCCCUGUGG	R641	1418	AUGACUUGGACCGCGUAGC
F642	1145	CCUCCCCACCAGCAUGUUT	R642	1419	GCAUCCUACCGUUGAAGCACT
F643	1146	GGCUUUGGUGAGAUCCAUUGAC	R643	1420	CACCUGGAACUUGGUCUCAAAGAUT
F644	1147	GCAUGUACUGGUCCCGCAT	R644	1421	AU UCCUACCGGAAGCAGGT
F645	1148	UGGUUCUGGAUCAGCUGGAUG	R645	1422	AUGACGGAAUAUAAGCUGGUGGT
R646	1149	UGCCAACAUGACUUACUUGAUCC	R646	1423	AAAAUAUCCCCCGGCUUGUGAG
F647	1150	GGACUAGGCGUGGGAUGUUUUT	R647	1424	GAAGAAGAUGUGGAAAAGUCCCAAUG
F648	1151	AGUGGAUCCCCUCUCCACC	R648	1425	GUCCCUGGCUGGACCAA
F649	1152	GAGGUUUUCCAGCACUCUGACAUAT	R649	1426	CACACAUUGGAGCAUGCCAUUC
F650	1153	CGGUUGAAUGUAAGGCUUACAACG	R650	1427	AGCCUAAACAUCCCCUUAAAUUGGAUT
F651	1154	GAACGGGAAGCCCUCAUGUC	R651	1428	CGGCUUUACCUCCAAUGGUG
F652	1155	CCUUACUCAUGGUCGGAUCACAAAG	R652	1429	GCAGAGAAUGGGUACUCACGUUUC
F653	1156	CCCUUUCUCCCCACAGAAAC	R653	1430	UCAGCCUGUUUCUGGGAAACT
F654	1157	GUAGAGCAAAUCCAUCCCCACA	R654	1431	UGGAGAGAGAACAAAUAAAUGGUUACCUG
F655	1158	UGUGCUUUUAGGGCCCACC	R655	1432	GAUUCUUAUAAAGUGCAGCUUCUGCAT
F656	1159	UCUGUUCAAUUUUGUUGAGCUUCUGAAUT	R656	1433	CAGACGUCACUUUCAAACGUGUAT
F657	1160	UCAGUGUUACUUACCUGUCUUGUCUUT	R657	1434	CAGGCUCAGGACUUAGCAAGAA
F658	1161	UGAAUUAGCUGUAUCGUCAAGGCA	R658	1435	UAAGGCCUGCUGAAAAUGACUGAA
F659	1162	UGUUUCUCCCUUCUCAGGAUUCCUA	R659	1436	AGUCCUCAUGUACUGGUCCCT
F660	1163	AAACCCGCAAUCCGGAAC	R660	1437	CUGAUCUCGCCAUCGCUGUA
F661	1164	CCCUCCAACAUCCUAGUCAACUC	R661	1438	GUUCAUACCGACAUGUAGGACCUT
F662	1165	GCUAGAGCUUGAUGAGCAGCAG	R662	1439	UCAAAGUCGUCAUCCUUCAGUUC
F663	1166	CCAUGGAGUCGAUGAGCUGG	R663	1440	CCUCCAGAUGUGAAGCCCT
F664	1167	GCCCAGCUCUGAGAUCCUUUC	R664	1441	GCUGGAGGAGCUGGAACUT
F665	1168	CAUUUCUGACAACUGAACUGCUCUC	R665	1442	UAAACAGGAGCACGAGGAUGC
F666	1169	UUACCAGCUUGUUCAUGUCUGGAUUC	R666	1443	UAUUCAUCACGGCGCGCUT
F667	1170	ACUGAGCUUGUUGGAAUAAGGAUGUT	R667	1444	GAGUCCAGGAGAAAAUUCACAUGAGG
F668	1171	UUGUAAGUGCCCGAAGUGUAAG	R668	1445	ACAACCCACUGAGGUAUAUGUAUAGGUAUT
F669	1172	UACGCAGUGCUAACCAAGUUCUUUC	R669	1446	AGCACAGUGAAUUUUCUUGCCAUC
F670	1173	CAGUCAAGGUUGCUGAUUUUGGUC	R670	1447	GGUGGUAAACUUUUGAGUUUGCAGA
F671	1174	UAUGGAUGUUGCCAAGCUGUAUUCUG	R671	1448	GGGAAGGAGUGGUACAACAGAT
F672	1175	GGUGGUCCUACCAUACAUGAAACAT	R672	1449	ACAGCUAGUUUGCCAGUUAGUAAGC
F673	1176	GCAAGCAAAAAGUUUGUCCACAGAG	R673	1450	CACUUAAUUUGGAUUGUGGCACAGA
F674	1177	ACAUCUCUCACCUCAUCUGUCCT	R674	1451	CUCUUGUCAUCAGCUCCCAGA
F675	1178	UCCCUGUAGUCCCGGAUGAG	R675	1452	GCGCCAGCAUCCAGAGAUAC
F676	1179	AAUUGUUGCCAUUUCAGGGUUUCUG	R676	1453	GAGCGUGUGAUGCAGCUCUT
F677	1180	CUCACCUAUCUCCCAGGCCUAAAAUA	R677	1454	GUUUGACCGAAGAACCAAUUAUACCC
F678	1181	ACAAACGAGAUGCCUCUUCCAG	R678	1455	GAUGCUUCUCUCCUUCUUCUCUUGG
F679	1182	GGCUGUCGUGGUAGACUUAGA	R679	1456	UUCCCCAACCCACAUUUCCUUUAUAG
F680	1183	CUGAGUGUAUCCUGGAGGUUGUUG	R680	1457	CCAAAACCCUCCUGAUGUACACG
F681	1184	GCUUGGUUCUGAUGUUUGUAGUGUAG	R681	1458	GUCACAGCUCCAGUGUCUGUC
F682	1185	UCCUUGUUGGUGUCCAUUUUCUUGT	R682	1459	GAGAUCCAGGCUACCUGGUAUGAG
F683	1186	ACAUGCCAUCAUUCUAGGAAGCUC	R683	1460	AAGGACGACCCAGAGCUGAT
F684	1187	CAGGACCCGCUUCUCUGAAAG	R684	1461	AAAUUAAAAGGCAAGUGGACUUCGG
F685	1188	AAGACCCCUUUAACUCAAGACUGC	R685	1462	CUGUUGGUGAAGCUAACGUUGAG
F686	1189	UGCUCCAUGAGGAGACACC	R686	1463	AAAAUGGGAAAGGUAUCCAGCC
F687	1190	AAUGUAACCUUGCUAAAGGAGUGAUUUCT	R687	1464	CCACAGAAACAACAUCGAUUUCUUCC
F688	1191	AACUGGCAAAUAUAUCAUUGAGCCAAAUC	R688	1465	ACAGGGAUGGUGGUGGUT
F689	1192	GGUGUGAAAUGACUGAGUACAAACUG	R689	1466	UUCUGGAUUAGCUGGAUUGUCAGUG
F690	1193	AUGGUGAAACCUGUUUGUUGGACAT	R690	1467	GGCAAAUACACAGAGGAAGCCUT
F691	1194	CCUGCUCAUGGUCUUUGAGUAUAUG	R691	1468	AUGUCUAUAGGGAAGGGAAGACG
F692	1195	GCCACACGCAACUGUCUAG	R692	1469	GUCGGUGCUGUAGAUAUCCCT
F693	1196	GACAAUCCU UGCU UACCUGAGGAAC	R693	1470	ACAUUGUCAAGUUCUAUGGAGUGUGC
F694	1197	GCUCGGGAUCCAUAUGUGGUAAT	R694	1471	CUGGCUGAAGGUGGGUUUGAUT
F695	1198	GGCCCUAUACUUAGGCCCUUUT	R695	1472	AAGUCACACGGCCCUCC
F696	1199	AACUCACGGUGGCUGCT	R696	1473	UUGUUCUCAUUGGCUUCAAAGAUCUUUA
F697	1200	UGUCCUGGUCAUUUAUAGAAACCGA	R697	1474	UCUCUUGGAAACUCCCAUCUUGAG
F698	1201	UCUCAUGUCUGAACUGAAGAUAAUGACT	R698	1475	UGAGCCCACCUGACUUGG
F699	1202	UUGGUAGCUCAGCUGGACUGAUAT	R699	1476	ACAUGAGAGCUUGUUUUUCACUGG
F700	1203	AUGAAGCAGGCUGAUACUACACAG	R700	1477	AGAGUGAUCUCUGGAUGUCGGAAUA
F701	1204	UUGUGAAGAUCUGUGACUUUGGC	R701	1478	ACCAGUGAGGGAAGUGAGGAC
F702	1205	CCUUUGGGUUAUAAAUAGUGCACUCAGA	R702	1479	UAAGCAUCAGCAUUUGACUUUACCUUAT
F703	1206	GGGAAGAAAAGUGUUUUGAAAUGUGUT	R703	1480	CAAACAAGUUUAUAUUUCCCCAUGCCA
F704	1207	UGGCUUUGAAUCUUUGGCCAGUA	R704	1481	GAUUUGAUCCAGUAACACCAAUAGGGUT
F705	1208	GUCGAGGCAAUGGAAAAGCUC	R705	1482	AAACACAAACUAGAGUCACACACCUT
F706	1209	AGAACAGCUCAAAGCAAUUUCUACA	R706	1483	AGCACUUACCUGUGACUCCAUAG
F707	1210	AGCAAGAGGCUUUGGAGUAUUUCAUG	R707	1484	UUGUGUGGAAGAUCCAAUCCAUUUUUG
F708	1211	UGUUCAUGCUGUGUAUGUAAUAGAAUGUT	R708	1485	AACCAUAUCAAAUUCACACACUGGC
F709	1212	CUGGAAUGCCAGAACUACAAUCUUUUGA	R709	1486	CUCUUGCUCAGUUUUAUCUAAGGCUAG
F710	1213	CUCAAGAAGCAGAAAGGGAAGAAUUUUT	R710	1487	CAUACCAAUUUCUCGAUUGAGGAUCUUUUC
F711	1214	UGACAGCCAUCAUCAAAGAGAUCG	R711	1488	CCGCAGAAAUGGAUACAGGUC
F712	1215	GGGAUUUCCUGCAGAAAGACUUGA	R712	1489	AGAAAAUCAAAGCAUUCUUACCUUACUACA
F713	1216	AAGGCACAAGAGGCCCUAG	R713	1490	UCCAGGAAGAGGAAAGGAAAAACAT
F714	1217	ACCAAUGGCUAAGUGAAGAUGACAAT	R714	1491	AUUUGCCCCGAUGUAAUAAAUAUGCAC
F715	1218	AGGUUAUCUUUUUACCACAGUUGCAC	R715	1492	GUCAAGAUCUUCACAAAAGGGUUUGA
F716	1219	UUUUCUGUCCACCAGGGAGUAACUA	R716	1493	GCCACUGGUCUAUAAUCCAGAUGA
F717	1220	GACAAGUUCAUGUACUUUGAGUUCCC	R717	1494	GCAUCUUGUUCUGUUUGUGGAAGAA
F718	1221	AGCAAAUAAAGACAAAGCCAACCG	R718	1495	UCAACAACCCCCACAAAAUGUUT
F719	1222	AGUUUAAGAUGAGUCAUAUUUGUGGGUUUT	R719	1496	UGGAUUUGACGGCUCCUCUAC
F720	1223	CUGACCAUGUGGACAUUAGGUGUG	R720	1497	UUAACACCUCCAGUCCCUCAUCUG
F721	1224	CCUUCCCUCGGGAAAAACUGAC	R721	1498	UAAGAUGUCCACUGCUGUUCCUUCAUA
F722	1225	GUUUGGUUUUGUAGGUCUUGUGGAUG	R722	1499	CU UCAGCCAAGGCAGCAAUG
F723	1226	GAGGUGGCCUGAUCUUCACAA	R723	1500	GAUAUGGAUUCACACAGACACUAUCACA
F724	1227	CGCUUAUGCAUACUCAGGAUGAGUT	R724	1501	CAAGGUGUUUCUUUGAUGCUCUGT
F725	1228	UAAGGUUCCUUCAAGCUGCCCUA	R725	1502	CCUGUGGACAUUGGAGAGUUGAC
F726	1229	CAUGGGAGGAUGUUCUUUCCCAUUT	R726	1503	GAACCUUAAAUGUCUCUCCUACCUGA
F727	1230	UUUUCUUCCUAAGGUUGCACAUAGG	R727	1504	AAGGCACCUGACCCAAACA
F728	1231	AUUUUUGGCUUCCUGGCCUUT	R728	1505	GCACAUAGUCCCGGAAGCUG
F729	1232	GGAAAGCCUCACCUGUCUACG	R729	1506	UUCUUGAUCUCACAGUCAGGGAUG
F730	1233	UCAAGAAUCGCCCGAGCC	R730	1507	AUGAGCAGCGUGGCCUT
F731	1234	UUGGUUCGGACAGACAACCC	R731	1508	UAGCUGUGCAUGUCCUGGUG
F732	1235	CUCUGCACAGCUCCAAUGAGAC	R732	1509	UAGGUGAGGACCACAAACCAAAC
F733	1236	GCUACAAGAACUACCGAUACCGT	R733	1510	UGGUCUUCACUCACCUCGGAT
F734	1237	CUCGGAGAGGAGCCAUACUG	R734	1511	UUCCUCCAGAAGCUUGAACUCT
F735	1238	UAUAAUGACAGUUAACCCUGCCAGGA	R735	1512	CCCAAGCCUGGGACCUCUAUUAT
F736	1239	AGGAAGAGCACAGUCACUUUGA	R736	1513	CAUGCUGGACCUUCUGCAC
F737	1240	CAGUGGAGCGAAUUCCUUUGGA	R737	1514	AGACUGCUAAGGCAUAGGAAUUUUCG
F738	1241	UUGGGUCGUUGGGCAUUCC	R738	1515	UUUGACUCUGUCUCCUCUUGUCUUCT
F739	1242	CAGUUCACAGUGCAGCGAAAA	R739	1516	GAGAUGAAGCAAACAACAGUGGAG
F740	1243	AAAUAUCUACACACAGGUCUACAAGGUC	R740	1517	AUUUCAUGCAAACUAGAUAACUACCUGUAA
F741	1244	CAUCCGGGCUUUACGCAAAUAA	R741	1518	UGGAGUUUGUCUGCUGAAUGAACC
F742	1245	GCCUCCUUCAGGAAUUCAAUCUUCT	R742	1519	AGCUCACAGAAAUGUCUGCUAUACUG
F743	1246	AUGAGUUCUGGGCACUGGG	R743	1520	AUGAGGAGUGUGUACUCUUGCAUC
F744	1247	GAUGCAAACUCUUGCACAAAUGCT	R744	1521	GCCAAGAGUUACGGGAUUCCAT
F745	1248	GAACCCCGAGGGCAAAUACAG	R745	1522	AGGAUGCCUGACCAGUUAGAGG
F746	1249	CAGUUCGUGGGCUUGUUUUGUAUC	R746	1523	AAAAGACUCGGAUGAUGUACCUAUGG
F747	1250	UUAAAGCUGGCUAUGGCACCUG	R747	1524	CACUCACCCUGGAUGUCUUCG
F748	1251	CAUCUCUCACCAUCCCAAGG	R748	1525	CACCGUAGCUCCAGACAUCA
F749	1252	AUACGCAGCCUGUACCCA	R749	1526	AAGGAGAAGAGGACAGCGG
F750	1253	CACCUCUCUCAAGAGUUUGGAUGG	R750	1527	CCUGCACUUCUAGGCACUUACUAA
F751	1254	AGAUUGCGAGAGAGCUGCAT	R751	1528	GGCACU UGCACAGAGAUGAT
F752	1255	CUGUGCUGCAUUUCAGAGAACG	R752	1529	AUUUGAUGACAUGUGGGUGGUUG
F753	1256	AAGACCCAAGCUGCCUGAC	R753	1530	GGAGCCGUAUUUGGCGT
F754	1257	GCUAUUUUUCCUCACAGCUCGUUC	R754	1531	CCUCUUCACGUAGGAAUCCUCUUC
F755	1258	CUCCUUCCUAGAGAGUUAGAGUAACUUC	R755	1532	AUCACUUUGCGUGGUGUAGAUAUGAT
F756	1259	GAGCCUGUUUUGUGUCUACUGUUCUA	R756	1533	AGGACUCUGAAGAUGUACCUAUGGT
F757	1260	CUCUUGCAGCAGCCAGACT	R757	1534	ACAGUUUCCAUAGGUCUGAAAAUGUUT
F758	1261	CCAUGGGACUGACUUUCUGC	R758	1535	AGCCCAACCCUUGUCCUUAC
F759	1262	GCUGAGGACCUGGUCCUCT	R759	1536	GGGACAGCAUCAAAUCAUCCAUUG
F760	1263	CUGCACCAGCAGCUCCUA	R760	1537	CCAGACGGAAACCGUAGCUG
F761	1264	CCCGGACGAUAUUGAACAAUGGT	R761	1538	GGAGCAGCCUCUGGCAUT
F762	1265	AGCCUCACCACGAGCUG	R762	1539	GGCAAGGAAAGGUGAUAAAAGUGAAUCT
F763	1266	CACCUUUCCUUGCCUCUUUCCUA	R763	1540	ACUUGAUAAGAGGUCCCAAGACUUAGT
F764	1267	CUCAAGGAUGCCCAGGCT	R764	1541	CCUAUGGCUUUCCAACCUAGGA
F765	1268	CCUCCCUGCUUCUGUCUCCUA	R765	1542	CCCUUCUGUCUUGAACAUGAGUUUT
F766	1269	CCAGUUGCAAACCAGACCUC	R766	1543	UGUGGAGUAUUUGGAUGACAGAAACA
F767	1270	ACUCCACACGCAAAUUUCCUUC	R767	1544	AGGCCUCUGAUUCCUCACUGAT
F768	1271	AGGGUGGCAAGUGGCUC	R768	1545	CCUAGGUUGGCUCUGACUGT
F769	1272	GAGGCUCCCCUUUCUUGC	R769	1546	UGCCUCUUGCUUCUCUUUUCCT
F770	1273	CUGUGACUGCUUGUAGAUGGC	R770	1547	UUCCUACAGUACUCCCCUGC
F771	1274	CUGUCGUCUCUCCAGCCC	R771	1548	AGUCACAGCACAUGACGGA
F772	1549	GGAGGAGGCGAUGGCUACUA	R772a	1574	CUGCAGUUAGAGGUUGGUGACA
			R772b	1575	CCCGCCAAGCACGUAUACU
F773	1550	GGAGACCUACAAACUGAAGUGCAA	R773a	1576	CCGGAAGAGGAGUAGCUGAC
			R773b	1577	CUCCUAGAGUUUUUCCAAGAACCAAGU
F774	1551	CCAUGCAGAAUGCCACCAAGUA	R774	1578	AUUUGCAGCUACUACUCUGAACUGAA
F775	1552	CAGGCACUCCUUGGAGCAA	R775	1579	UCAGUGGGAUUGUAACAACCAGAAAU
F776	1553	CUGUUUGAAAUGAGCAGGCACU	R776	1580	GCACUGUCACCCCUUCCUUG
F777	1554	ACUGGAGGACCCGUCUUCU
F778	1555	AGACCUUAAGGGAACAGCUCUCAU
F779	1556	GUGGAGUCAUGCUUAUAUGGAGCAAA	R779	1581	GCUCCAUCUGCAUGGCUUG
F780	1557	GACAGAAAAAUAAUUCUGUGGGAUCAU
F781	1558	UCCUGAAAGAGAAAUAGAGGUUCCUGAU
F782	1559	GGTGGCCATAGGAACGCA
F783	1560	UGGAUGCAGAAACCAGAGAUCUAGU
F784	1561	CUGGUCCCCAGACAACAAGUAU
F785	1562	GAAGAUCAUGUGGCCUCAGUGAA	R780	1582	GGGUUGUAGUCGGUCAUGAUGG
F786	1563	GUCGAAAAUACCUUCAACACCCAAAUU	R781	1583	CCUGGCCCUUGAAGCACUA
			R782	1584	ACCCCAUCUUCCCCAUCCAU
F787	1564	CCAAAACUGCAGACAAGCAUAAAGAUG	R786	1585	CUACCUCACAGUGACUGCAGUUUA
			R787	1586	AGAGAGGAUCAGCGAGAGUGG
F788	1565	CAGGCAGAAGUUGAUCGACUCU	R788	1587	GUCUCGUUGCCCAAAUUGAU
F789	1566	AAAGAAGAGUGCACAAAUGUUAGAGGA	R789	1588	AGUGUUUUCAUUCGAUUCCUGUCUUCU
F790	1567	CCAGCUUCCUAUAACUUGGACGAU
F791	1568	GAACCACAUCAUGGUCUCUGUCU	R791	1589	GGUGAUGCCGUGGUUGAUGU
F792	1569	UCAUCGGGAAGACCUGGCUUA	R792	1590	AGUUCUCGCUUCAGCACGAU
F793	1570	GCUGCAGGACUAUGAGGAGAAGA
F794	1571	CUCCCAGAGACCAACG U UCA	R794	1591	UGGCCAAGCAAUCUGCGUAU
F795	1572	GGACCUGGACCGUGUCCUUA	R795	1592	UGCCAGGAUCAUAGCGUUUACAG
F796	1573	GGACCUGGACCGUGUCCUUA	R796a	1593	CUGGAGCAGGUCCACUAUAGGU
			R796b	1594	UCCUCACACCUGCUCCUCA
			R796c	1595	GCUGAUGGGUGGGCACUG
			R796d	1596	GGUCUACCAGGACUGUCCCU
F797	1760	CCCUUCGUAGACAUAUAGCUGUUCUC	R797	1597	GGAAGGCAGGAAGAUUUUCAAUCUC
F798	1761	UGGUGCUAGUUGCAAAGACACAA	R798	1598	CGUUUAUAAGCACUGUCACCCCUU
F799	1762	AGCGACGCCAUUGCUCAU
F800	1763	CCUCAACCAUUUCCGGCAAAU
F801	1764	CCAGCUCCCUGCGAAGAG	R801	1599	AGGAUGAUGGCACUGAACUCC
F802	1765	AAUCCCUGCAGUAGAUACGAAGACUA	R802	1600	CACGUUAGUUAGUGAGCCAGGUAAU
F803	1766	AGACCUUGCAGAAAUAGGAAUUGCU	R803	1601	CUCAGGGCUCUGCAGCUCC
F804			R804	1602	CCUCCGGAAGGUCAUCUCA
F805	1767	AAAGAAAAGACAGUUGGAGGAAUCUGU	R805
F806	1768	GAAGAAAAUGAAAAGGAGUUAGCAGCAU	R806b	1603	CUCCUAGAGUUUUUCCAAGAACCAAGU
			R807	1604	GAACCAAGUUCUUCCGAGGGAAU
F807	1769	AGUGGCAAAAGAACUUCAGACUUUACA
F808	1770	GCGCUGCUCAGAAGCAAAA
F809	1771	GUAGAUCGCAUAAAGGAAGCAGUCA	R809	1605	ACAGCGGCUGCGAUCACC
F810	1772	GGAAGCAGUCAGGUCAAAGAAUAUGG
F811			R811	1606	GCUGACUGCACAGGACAGG
F812	1773	CAAGCAGAAACACUGUACAAAGAGAUU
F813	1774	GAGGGCGAGCUGCAUGAU	R813a	1607	CGAGACCCCAAAAGGUGUUUC
			R813b	1608	UCCACAUUUGUUGAGCACAAGGA
F814	1775	CACAUCUUCAGGUGCUGGAUUUUUC
F815	1776	CUUUUGAAAAGCCAGUGAUGAUCUCAA	R815	1609	CACCUUUAACUGCUUCAGGGUCAAUAU
F816	1777	GCACCUUGACUUUAAGUGAGAGCA	R816	1610	UGUUGUCCCGUGGCCAUU
F817	1778	ACAGCACUGUUAUUACUACUUGGGUUUU	R817	1611	GGCAUGAACCGUUCUGAGAUG
F818	1779	CAAGCUCCUUACAUACCCAGCA	R818	1612	CCAAAUUCGCCUUCUCCUAGAGU
F819	1780	GCGUUUCCUCGCUUGCAUU	R819	1613	CUCCUCUGCACCAAGGUAAACA
F820	1781	CGGGCAGGAATCTGATGACTTT	R820	1614	UCCCUUCUAGUAAUUUGGGAAUGCC
F821	1782	GCAGGGCAGCAACAUCUUUG
F822	1783	GGCUCCUGAGACCUUUGAUAACAUAAC
F823	1784	CGUGUGCUCCCUGGAUAUUCUUAGUA	R823	1615	UCAGCUUUCUCCCACUGUAUUGAAUUUU
F824	1785	CUGGCUCCGGGUGACAGC	R824	1616	UCGGAAGGGCUGUGGAAUUG
			R824b	1617	CGUAGGCACACUCAAACAACGA
F825	1747	CUGGCUCCGGGUGACAGC	R825	1618	CUGAUUUCUGAACAUGGACUGUGG
F826	1748	GACUCCCAUGACCCCCAUC	R826	1619	ACGAAGUGCAAUGGUCUUUAGGU
F827	1749	AAAAAUGUUAUGUCAGCGUUUGGCUUAA
F828	1750	GUAGGCGCGAGCUAAGCA	R828	1620	GUGAGUCAUUUGUCUUGCUUUUGGU
F829	1751	CAGGUCAUAUUGAACAUUCCAGAUACCU
F830	1752	GGUCCUGACGCAGGCUUC
			F829	1621	GACAGUCUGAAUCAUGUCCUUCAGU
			F830	1622	GGGCUGCCCACCAUCUUC
			F831	1623	UCAGCCUGAUAGUCUGGUACAAACU
F831	1753	GUACCUGCAUCAACCCCUCUAA
F832	1754	CAGAGACCCGUGCUGAGUUU
F833	1755	GGAGAGAAGAGUGCACAAUACCA	R833	1624	CCUCCACCUUGGGCUACUCA
F834	1756	CCUGUAAUCCCUGCACUUUAGGA	R834	1625	GGGUGAGCCUUGACACACA
F835	1757	ACUUUCCAGUUGAGCAUCCCAAAUU	R835	1626	CAGGGAUCAGUUCAGCUGUACC
F836	1758	CGUCAGCGUGAUAUGUACCGUAUUUUAU
F837	1759	CACCUCAGUAAUAUGGAAGUCCAAGUU

TABLE E

Primer Name

SEQID

Primer Sequence

Primer Name

SEQID

Primer Sequence

Primer Name	SEQID	Primer Sequence	Primer Name	SEQID	Primer Sequence
F838	1627	UGGGCUCUGUAAAGAAUAGUG	R838a	1665	AUCAGAGCU UAAACUGGGAAG
			R838b	1666	AUCAGAGCU UAAACUGGGAAA
F839	1628	UGCACACUUGGACAGCAUUUC	R839	1667	GUCUCAGUUUUCCUACCUGUAAAAUGAAG
F840	1629	CCAGGACCAAUCUGGUCACAAACAUA	R840	1668	ACUUAUUCUGACAGUUCUCUUUUUCCCT
F841	1630	GGUGGGAGGAAAAGACAUAGGAT	R841	1669	GGUGGCAGUGAGCUGUAACAGUA
F842	1631	CUCCAGAGAGAAAGAAUCAACAGG	R842	1670	UCAGCCUCCAUAUCACUUGAGC
F843	1632	GCAUCCGUGACUCUCUGGAC	R843	1671	AACUUGGGUUGAGCCAUAGGC
F844	1633	UCAGUGAGCCAAUUCCUUGUAAUAACUC	R844	1672	CCUGGUUCCAUGGAUUCCACAUUAAGA
F845	1634	CAGAUCCCAAGCUCUUCCUCUT	R845	1673	GCGUUUGUGUGUGCAUCUGT
F846	1635	GUUCAUGCCACUGCACUUCACT	R846	1674	UCUGGUGUGUGGAGAUGUCUUAC
F847	1636	GGUGCACCCAUUACCCGAAT	R847a	1675	GGCUGCAAAAAGCUAUAAUUGUACC
			R847b	1676	GGCUGCAAAAAGCUAUAACUGUACC
F848	1637	UCCCCAUAUAAGUUCAAGCCUGUGT	R848	1677	UGUGUUAGUCAGGAUUCUUCAGAGA
F849	1638	UUGUAUAGCUACAGUUUUUCUGUUGGT	R849	1678	UUCAGUUAUAUGUGUAUAAAUGUGUGCAUUG
F850	1639	UAAAUAUGUGAGUCAAUUCCCCAAGUG	R850	1679	CUCCAGAGACAGACUAAUAGGAGGUA
F851	1640	GGCUAGAUUUUCCCCGAUGAUAGUAGT	R851	1680	CCUGUGCCCAAGUUGAGAGAAT
F852	1641	GGCUAGAUUUUCCCCUAUGAUAGUAGT
F853	1642	CAGUAAGUUAAAGGAUUGCAGGAG	R853	1681	UAAUCCAGCUGUGGGAGGGA
F854	1643	UGUGUAUAUGCAUUUACCUGUGAGUAUG	R854	1682	GGUGCUAGGUGUGCUCAGGA
F855	1644	UGUAACAAGGGCUACAGGAAUCAT	R855	1683	CUUCACUCUCCUUCCCAAAUGUUUAUG
F856	1645	GGGCAUCUCUUAUACUCAUGAAAUCAA	R856	1684	CUAUGAUUCCCCCACUGCAGUC
F857	1646	CUAUGCAGAAGAAUGAACCAGGGAT	R857	1685	AGACCCCAAAAUUACUUGAGCCAAUUUA
F858	1647	UGAUUCAUUUCCAUAGGGUAAGUGAAAA	R858	1686	ACUUCAACUUCAAUUCAUCCACUGAAA
F859	1648	GACAUUAUCACCAAUUUUUCUAGACG	R859	1687	UGCUUGCCUGUAUGAAAAUAUCUC
F860	1649	GACAUUCUCACCAAUUUUUCUAGACG
F861	1650	UGUGACAAGGGUGAUUUUCCUC	R861	1688	UCCAAUCAUAGCCACAGUUUACAA
F862	1651	CAUAAUUGUAUGAGCCACUUCCCAT	R862	1689	GCACUCUUAUUCAUCUAGUUGCCUGT
F863	1652	AGACUCACAAUGUACAAAAGCCUAUT	R863a	1690	CAUCAUGUGAGCCAAUUCCUCUC
			R863b	1691	CAUCAUGUGAGCCAAGUCCUCUC

Primer Name	SEQID	Primer Sequence	Primer Name	SEQID	Primer Sequence
F864	1653	AAUAUAUAUAAAGGGUAUGAUAGAACACUUGUC	R864a	1692	UUGCACCAAAUAUUGGUAAUUAAAUGUUUACT
			R864b	1693	UUGCACCACAUAUUGGUAAUUAAAUGUUUACT
F865	1654	GGCCUGGCAACUUAUAUGUAUUUUUGUAUT	R865	1694	CACUGUAUCGUAUCCCAUUGCG
F866	1655	GGCCUGACAACUUAUAUGUAUUUUUGUAUT
F867	1656	CCAUCCUUAUCUCUUGUGUAUCUAUUCAUUCAA	R867	1695	U UGCAAGCAAU UGCCAUAGAGGGA
F868	1657	GAUUUGUCUGUAAUUGCCAGCAAAA	R868	1696	ACAGAUUAAACUGUAACCAAAAUAAAAUUAGGC
F869	1658	GAGCAAGACACCAUCUCAAGAA	R869a	1697	UGCCUAACCUAUGGUCAUAACG
			R869b	1698	UGCCUAACCUAUGGUCAUACCG
F870	1659	CAUGAUUGAUACAUGGAAAGAAUUCUCT	R870	1699	CCCAGGAGGUGGAGAUUGAA
F871	1660	ACCCAAAUCAACUCAACUCCAGUG	R871	1700	UCCAUGUACUUUGUCCAAUGCUGA
F872	1661	UUAGAGCAUUUAAAGUAAGCCACAGUGT	R872	1701	UGUCAACACGAUUAACAUGCAAAGA
F873	1662	CUGUACACAGGGCUUCCGAGT	R873	1702	CAAAAUUCAAAGGGUAUCUGGGCUCT
F874	1663	UUUCAGGGCUGUGAUCACUAGCAC	R874	1703	UGUGCGCUGGUCUUACUCCUGUT
F875	1664	AGAUACAUAGGUUAGAUAGAGAUAGGACAGA	R875	1704	GCCCUAGUGGAUGAUAAGAAUAAUCAG

Claims

1. A composition comprising a plurality of nucleic acid adaptors, wherein each of the plurality of adaptors comprise a 5' universal handle sequence, one or more tag sequences, and a 3' target nucleic acid sequence wherein each adaptor comprises a cleavable moiety;

wherein the target nucleic acid sequence of the adaptor includes at least one cleavable moiety, cleavable moieties are included flanking either end of the tag sequence and the universal handle sequence does not include the cleavable moiety; and

wherein at least two and up to one hundred thousand target specific adaptor pairs are included.

2. The composition of claim 1 wherein an optional tag sequence is included in at least one adaptor, and the cleavable moieties are included in the adaptor sequence flanking either end of the tag sequence.

3. The composition of claim 1 or claim 2, wherein the melting temperature of each universal sequence is higher than the melting temperature of each target nucleic acid sequence and each tag sequence present.

4. The composition of any of claims 1-3 wherein all of the adaptors comprise tag sequences having cleavable groups flanking either end of the tag sequences.

5. The composition of any one of the foregoing claims, wherein the plurality of adaptors capable of amplification of one or more target nucleic acid sequences comprise a multiplex of adaptor pairs capable of amplification of at least two different target nucleic acid sequences.

6. The composition of any one of the foregoing claims wherein each target specific pair of the plurality of adaptors includes up to 16,777,216 different adaptor combinations comprising different tag sequences.

7. The composition of any one of the foregoing claims wherein the cleavable moiety is

(i) within the 3' target-specific sequence;

(ii) at or near the junction between the 5' first universal handle sequence and the 3' target-specific sequence; and/or

(iii) at or near the junction between the 5' first universal handle sequence and the unique tag sequence, and at or near the junction between the unique tag sequence and the 3' target-specific sequence.

8. The composition of any one of the foregoing claims wherein each of the one or more cleavable moieties is a modified nucleotide, nucleoside or nucleobase not naturally occurring in the target sequence of interest.

9. The composition of any one of the foregoing claims wherein the one or more cleavable moieties is a uracil base, uridine or a deoxyuridine nucleotide within the 3' target-specific sequence and the junctions between the 5' universal handle sequence and the unique tag sequence and/or the 3'target specific sequence wherein the at least one cleavable moiety in the plurality of adaptors is cleavable with uracil DNA glycosylase (UDG).

10. A kit comprising the adaptor composition of any one of the foregoing claims 1, optionally further comprising one or more of an amplification reagent, a digestion reagent and a repair reagent.

11. Use of the composition of any one of claims 1-10 for preparation of a library of target nucleic acid sequences comprising:

(a) contacting a nucleic acid sample with a the composition of claim 1 under conditions wherein the target nucleic acid(s) undergo a first amplification;

(b) digesting resulting first amplification products to reduce or eliminate resulting primer dimers and prepare partially digested target amplicons, producing gapped, double stranded amplicons, then repairing the partially digested target amplicons; and

(c) amplifying the repaired target amplicons in a second amplification using universal primers, thereby producing a library of target nucleic acid sequences.

12. A composition comprising a nucleic acid library generated by the method of claim 11.

Drawing